Hello. So I received my Helix Rack today from Sweetwater and I'm sorry to report that my experience with the loops has been a really positive one compared to yours. This was the very first thing I tested as your post had me worried big time. Having amps in the loops, or using the 4-cable method, is going to be my primary setup.
Mind you that I can only compare it to a Digitech GSP1101, 2120, Boss GT-3, 5, and 10. The helix has to be the most transparent of all, closely followed by the GSP1101. The others I listed don't even come close. In one of the loops, I have a head switcher (Ampete Spyder which is the best switcher I've ever used!!!) and in the loops of the switcher I have a Mesa, Ceriatone, Diezel, and a Rhodes. All sounded and felt the same with the Helix as it was with my previous setup. I used the loop block instead of the send/return block...
I wouldn't say I'm a tone expert nor do I have perfect hearing. But with what I'm doing with the Helix, I'm really happy with it! Hopefully you can try a different Helix and have a better experience. Maybe try the rack in the future...