Hey Dug/Doug (LOL) - I have a guitar with the same bridge and neck Fishman's on the Ibanez you're looking at. I love that combo, but of course tone/sound is soooo subjective. The thing about the other stuff you're talking about in "A" is that it depends on many things and the pups. I do everything digitally, and "noise" is never an issue with any pups. I have those pups in an ESP 7 string baritone and they sound great doing really heavy distorted stuff and clean. Using the Helix, anything is easily doable. If you want an audio demo, I'll make one for you.
On B, that's a tough one. I'm someone who never uses the tone control on a guitar, while you use it all the time. My Helix presets are set for amp and speaker settings, along with effects, etc. I use diff cabs (I have a zillion IRs but figured out that Helix cabs as as good and better in many ways - my opinion) and cab settings to really affect tone and will throw in EQ if I really need to adjust highs. That guitar should have a money back guarantee (at least most places have that) so if you really miss the tone knob, you can pay shipping and send it back. I checked out the guitar and I like it!
And not having a tone knob is just a feature - I've seen other guitars like that. Unfortunately, there probably isn't room to add one in the cavity if you wanted to, but who knows. I build guitars and for me, doing the electronics is easy if you take the time to learn how to solder guitar electronics and go slowly.