The straightforward solution for me would be to do it outside, or otherwise increase the ventilation, and wear a VOC respirator.

With a good VOC respirator you won't smell a thing until you take it off again. Be sure to also have a layer of removable outer clothing that you can take off and leave somewhere to air out because clothes will absorb the volatiles and release them again.

Don't forget to cover your eyes and hair. Eyes are an easy path for volatile vapors to get into your blood, even without splashes. They just absorb the vapors directly from the air. Hair will absorb and re-release the vapors like cloth.

So put on clothing and respirator, go to work area and work, go to well-ventilated changing area, remove outer clothing and leave it there to air, go back into house and remove mask.

Good luck,

Laszlo

Why are you using penetrating epoxy?  That stuff is usually reserved for repairing areas of damage/rot.  The fumes are a result of the solvents that are added to get a really low viscosity which allows it to seep into the damaged ares.  For building, regular epoxy like MAS or West will provide excellent protection without the stinky solvents.  I use MAS and it is nearly odorless.  I also find that I get a nice ready to sand surface by using the "roll and tip" method. 

Picture is the interior surfaces of my GIS precoated with MAS prior to going 3D.

Smith's is the original formulation for cert. His website warns users about the stink if used indoors, recommends their winter formula as much for the vastly less obnoxious stink as for the benefits of proper curing under cooler temps:

"Restoration of wood inside a house, such as in a bathroom, a door threshold or the inner part of a window sill, should be done with Smith's Cold Weather Formula rather than Smith's Warm Weather Formula when the house is occupied, due to the much milder odor and more rapid solvent vapor dissipation of this version."

I've been using MAS LV for a few years now too, like its lack of odor though I'm still habituated to using a 3M respirator fitted with (minimum) 6001 cartridges. Seems to penetrate raw wood & ply well enough as long as the workpiece is 75° - 80°F.

From what little I've done with Smith's I can tell its job is to penetrate better than anything designed to work as an adhesive. Hope this helps....  

I've found very few references that show that "penetrating" epoxy really penetrates any better that ordinary epoxy. From my experience, a lightly sanded coat of properly cured MAS epoxy filled the pores of wood and made a very durable base of one-part polyurethane paint. As it is transparent, I would expect it to do just as well with varnish.

I definitely prefer epoxy to PreKote under paint. I'll never use PreKote again (unless I move to the desert).