I had something similar to your situation, before helix I had several rack preamps and a rack power amp, when I took the helix I did the test using the emulation of the premp (not the heads) and using the rack power amp that i had. I had evidence that the guitar power amp alters the sound in a similar way to a preamplifiers, so everything was altered by the power amp. I have replaced the power amp with another one with custom guitar power amp with more neutral sound but the character of the power amp always made itself felt, so i have replaced it again with an a HiFi integrated amp and a HiFi Spekaer solving everything with the IR.
A guitar power amp alter the sound like a clean channel of the preamp, but with slight differences on certain aspects.
PS: sorry for my bad english