I used the Behlen's stain (alcohol based) to color both filet "butter" and lapstrake seam-filling epoxy glue mixtures as I assembled my dory, which had stained hull panels.  I've not had any issues with epoxy setting up or with reduced strentgh (if there is any).  The stain will thin the epoxy mix very slightly, but that didn't seem to be an issue - can always add more wood flour, etc. as needed.

This worked very well to keep things matched and made the joints and filets blend in as nearly invisible from other areas of the stained (interior, upper 2/3rds) of the hull (the remainder of the boat is painted).  Behlen's does advertise some anti-fade properties to their stain - I'd be wary of what you use as a stain/dye.  I presume anything might fade with U/V, but I'm sure some colorants and colors worse than others. Like most all colors and U/V, I presume the red end of the spectrum fades most quickly (but even so, my color is "Blood Red."   

I never colored any of the epoxy used for GENERAL coating of the boat panels. I stained all the wood I wanted colored, and gave a clear epoxy topcoat prior to assembly. This works very well - the panels are probably very slightly stiffer during assembly, but that created no problem in making bends while stitching things together. The use of stain on any part of the boat does still require touch up to any areas that get sanded through after assembly during the build, and achieving a good match of touch-up areas is an art.  You do need to know that adding any color/stain anywhere adds a level of difficulty to the build and to repairs.  Nothing that can't be overcome, just be advised.

And finally, if you try to color any part of your boat by actually coloring the epoxy instead of staining the wood, I'd guess it would be best if the epoxy was the first coat, not last.  

And with all this said, I'd advise agains the whole idea because the thickness of the colored epoxy will definitely effect the depth/tone of the color achieved, and you'll never achieve a uniform thinckness of coating.

Doing a Google search for that question brings up a bunch of hits showing how it can be done, so yes it's possible.

BUT before you risk a future catastrophic failure I'd put the question to the tech staff at MAS first for their suggestions. After all they know best what goes into the bottles that get sent out to us, what their products may - or may not - be compatible with.   

   Good recommendations by spclark, of course, related to using Google and asking the experts.  In clicking his links, it reminded me that I forgot to mention one very important thing.  You'll have decide if you're trying to achieve a transparent color or an opaque color.  With the Behlen's, adding the stain did add a small level of opaqueness to the epoxy, and even more so when the fillers were added.  So unless you find one of those dyes online that works with the MAS and advertises itself as transparent (and you test it first?) be careful.  If you want to see the wood grain, I'm back to suggesting that you stain the wood first, then coat with clear epoxy/varnish.  The fact that my seam fill lapstrake joints and bulkhead & etc. filets are opaque isn't an issue with the overall "beauty" of the boat.  If you are putting on opaque epoxy, or even semi-transparent epoxy over the wood you're loosing the "pop" of the wood grain, and probably better to just paint.

I guess I should have been more clear about the desired finished product...

I was thinking along the lines of epoxy countertops, achieve an opaque, various colored marbling by using pigments.  Not planning on seeing the wood grain (though still undecided about doing just the sides and bottom and leaving the top wood-grain).

https://www.amazon.com/Metallic-Epoxy-Pigment-Bulk-Containers/dp/B01DAPPA92

Already sent an e-mail to MAS, and appreciate the feedback about effecting repairs.  Being in the middle of replacing a stringer and reskinning a SOF kayak, can definitely appreciate the repair/matching aspect.

Was still planning on varnishing over the epoxy resin for the UV protection.

   I've used black dyed epoxy in a situation where I didn't want to use paint (the epoxy is more durable) and was worried about dyeing the bare strips because the dye would have bled through t the other side which I wanted to finish "bright."

I used the System 3 additive. 
I didn't use it when laying up the glass over concerns that it would weaken the bond but I suspect this would have been fine. The mixing directions suggest a max amount to add to your clear epoxy without affecting the chemical reaction. 
I found I needed two rather thick fill coats to achieve an opaque black- even so it's faintly translucent. The first dyed fill coat looked terrible- uneven and patchy. So count on multiple coats. 
Good luck, Patrick 

I have never 'dyed' mas epoxy but got a pretty similar effect with colored additives.

i have a couple 'dyes' i have made with behlens stain mixed into wood flour and then left to dry (so i have basically little vats of different color wood flower) that i use to color epoxy.  i have made black epoxy with graphite as the additive.

i have some lighter colors that i have made with other additives....but never anything that was a liquid...all powders of some sort.

h