Good morning Fellow Knought! Be careful not to break wind inside your suit of armour, or you may pass out, Excellency!

All kidding aside, I was going to say the same as you when I first read the question... theoretically, any pedal should work with input from a piezo-eqipped classical guitar. HOW WELL the effect does its job, however, will depend on the nature of the tone shaping the pedal is designed to perform. Your Martin pickup is probably pretty "hot" compared to a lot of others, and you are right: the output from the Variax is not a  raw direct out from the transducer. The signal has already been processed quite a bit by the time it gets to the input stage of the pedal, and may not be delivering exactly the kind of input signal the pedal needs to work properly.

I also have to wonder what the effects chain looks like, and where the TRS cable enters the picture. Seems to me that the Variax would have to be powered off batteries for one to be able to insert a pedal into the signal chain. Seeing as there are so many REALLY knowledgeable electronics whizzes on this Forum, I will not embarrass myself with any further technically-related speculation in this regard.

Regardless of what the hookup looks like, I would still be starting from a premise like:

I want to add a lush, chorus effect to my Nylon sound. Can I do this with my existing Boss pedal? If so, can I connect my guitar directly to the pedal, or should I route it through the effects loop of my amp?

This type of question, I feel, would generate a more fruitful discussion, although I can see that it might be useful to know, in general terms, how to correctly hook a Variax up to a standard pedalboard...

My $0.02/FWIW/YMMV

JellyWheat