What do the native sounds in the Variax sound like? Our guy used the 12 string a lot and the old Les Paul. He HAD the Helix but he didn't always have it engaged.
I guess the realistic answer, (without trying to make it sound like the Helix/Variax combo is the greatest thing since sliced bread)is to say that modeling provides a convincing representation of a guitar that was modeled under specific settings. If you have ever used Impulse Responses, you have noticed that a typical set of IRs will include a LOT of different files with slight differences in one setting. Differences in mic distance from the speaker cabinet, or mic used for an acoustic guitar. That is a limitation of modeling.
A good amp with a good guitar gives your guitar player all the flexibility he needs to extract the full spectrum of sounds out of his gear, and that's probably why he doesn't always use the Helix. Given enough time to tweak parameters by trial and error, it might be possible to get the same sound out of the Helix, but your guitar player probably has an understanding of his gear that lets him get from idea to tone with a lot less effort.
But I'm not a pro by any means. For me, it's way better than anything else I've ever used to duplicate sounds on the songs I'm trying to replicate.