keeping fine details?

I am assuming home casting here, if you intend to have a company doing the casting you should ask their help, as their casting methods and materials may vary.

There may be a lot of different ways to do this, but here are my thoughts:
I would cast the "coin" separately and then glue it into the head before adding the clear resin.
The main reason is to minimize waste, as the small details in the logo have a higher risk of trapping bubbles. Suppose the whole head cast perfect, except for the logo? Would you have to discard the entire head? Or would you need to spend a lot of extra time fixing it every time it happened?
Another thing to keep in mind is that smaller parts tends to be easier to cast than big ones, because of less heat building up during curing and that means less risk for gas bubbles to form within the piece as well as less risk of "pock marks" if there are hidden bubbles in the mold.
This also gives you the option to make the signature coins in any colour, with may be nice for white and other light colours that may be very hard to read otherwise.

Even if you want to cast the parts together, I would still make them separately up until the very last step. That way you get a lot better control over the amount of primer you use and will make it easier to remove if you add too much.

I would definitely use primer on the polymer clay before making the mold.
Polymer clay, when properly cured is fairly stable (at least short term), but there is really never any way to be 100% sure. It could still be sweating chemicals that may react with the silicone.
You can test this, of course, but that is only a short term evidence. There is no way to tell how the mold will behave long term. If that happens you can make a new mold (always save your master), but that is a lot more work and expense than blasting the piece with a layer or two of primer.

Other than that, for the general topic of avoiding loosing tiny details:
Just spray those parts less. If you have large smooth surfaces (head back, thigh pieces etc.) that need a very good surface, spray those generously first. Prime and sand as many times as it takes. Then work your ways to smaller and smaller parts using lighter coats and more care.
You may also be able to start with a finer grit sandpaper than you use for surfaces that you want to smooth out.
Sometimes things like fingernail definition will be lost under the primer and will need to be carved, sanded or filed back, but that is usually a matter of removing very litte actual material, so it doesn't take too long. Just pay attention to when something fills in and correct it as soon as the primer is dry, before the next layer, so that you don't accidentally fill things in completely.

Finally, thoughts about clear resin and home casting.
Clear polyurethane resin does exist, but is notoriously difficult to cast. The place I buy my resin from only sell it to professionals or experienced hobbyists with professional grade equipment for that reason.
There are other types of clear resin, such as acrylic, that can be a little easier to work with, but I would be hesitant to mix materials in the same piece like that without at least some thorough research into how they are likely to work together. You don't want to fill in a hole only to find out that your filling expands or shrinks with age or that the curing process of the one causes some sort of reaction in the other.

On the previously mentioned topic of waste, what do you do if the clear layer does wrong? This is, if I understand you correctly, the very final step of the production so all the other time and materials will still have been put into it, what will you do if you get bad bubbles or a batch that wont cure? Does that mean the entire batch of heads are essentially lost or do you have some plan for preventing that? No caster have a perfect success rate, after all.
Also take the future into consideration. Most clear resins will age more visibly and sometimes faster than opaque resin, simply because of light penetrating deeper into it. Will your signature still be visible in 20 years, if the clear layer have discoloured, yellowed or clouded?
On the same note, how will it work with faceups? I know you said it will be on the inside, but it's still worth at least think about how it will behave together with commonly used materials. The sealer will make the surface matte and may give it a frosted look, will it still be readable? And what about the solvent used to remove the faceup? Polyurethane is tough stuff and very resilient to solvents, but acrylic is a lot more sensitive.

 

Epoxy is probably a good choice. I find no information on shinkage on the page you linked, but since they recommend working in thin layers and the time between layers seem to be a bit sensitive, it sounds as if there will be a bit of shink or distortion. But for your needs it may be too little to matter.

Also be aware that it does acctually say "for industrial use only" but I have to admit I don't know what that means in this context. It's right below the link to the MSDS.

 

You could try making the original coin in wax. It doesn't need priming before making it's mold, but you'll need a heat source and metallic tools to work with it.

 

May it have anything to do with the fact that the product is corrosive?
Perhaps you should contact Smooth-On and ask for a clarification, it's not a good idea to ignore a line like that just because there are bigger warnings elsewhere.

 

I thought to insert a wax seal into my doll's head too, your idea to cover it with clear resin is good, but you'll definitely need a pressure chamber, vacuum is useless with epoxy and even if smooth-on says that it will be bubble free is not fully true, there will alwais be some bubbles due to catalysis. I never tryed the one you linked, if you make a small layer you can try using a oxy flame but I personally don't raccomand it and It's not professional.


Anyway, I don't know if you resolved but if you make the seal in wax there is no need to primer it, it's already smooth, you can primer the head and the add it before the cast.

There are silicons made to tolerate low-melting metals, like pewter. They start to broke after 10/15 copies, but if you have to make only a coin it's perfect. It takes even small details, if you pre-heat the mold hot metal will set into every detail without struggle, but you need to be confident with bivalve molds and the silicon catalyzer is really toxic and gives migraine if you don't use professional masks. If you don't want to make everithing by yourself there are sellers on etsy that makes custom conis, I guess.

Don't know if this can be helpful, good luck