I think it's going to depend largely on how you ask.
There are a couple of problems with simply comparing groupsets.
First, one component on one bike might be lower quality while another on the same bike might be higher. This is fairly common when comparing similar quality bikes.
Second, comparing one company's components to similar quality components from another company is not as straight forward as "this one is better than that one." Usually, it's more along the lines of "this is nice about this one, but this other thing is nice about this other one."
As far as how well a question like this fits into the site...
If you just want to compare the two groupsets on the bikes you've shortlisted, it's probably too localized. Those two bikes will probably each change a component or two when next year's product line rolls out and the question will no longer be valid.
On top of all that, there's a lot of subjectivity in comparing one brand to another. There's a lot of brand loyalty regarding bike components. Sometimes that brand loyalty is well warranted and reasonable, other times it seems to come from a more emotional place. The truth is that most companies make good parts and crappy parts and everything in between. But you still find people who say that company x is awesome and company y sucks.
Finally, Bontrager is a subsidiary of Trek. They mostly make static parts with no moving parts like seatposts and stems. Shimano is an independent company that makes fishing and rowing equipment as well as bike parts. They basically specialize in small parts with a lot of moving pieces. Their bike line consists of mostly drivetrain components. There's not a whole lot of overlap between the two, wheels being the big exception. And I don't see any overlap on the two bikes you're comparing so I'm not even sure what you're wanting to compare.
All of that being said, I think that there's probably a way to ask about comparing components in a general way that would both help future visitors and get the information you need to make an informed purchase.