If you don't have stack and reach values available (as on the Mares), BB drop needs to be accounted for in your calculations to ensure that comparisons you make using HT, TT, ST, fork length etc. actually work. This is why BB drop is a listed value on both of the geo charts you have access to for these two bikes. So when I say control BB drop on the spreadsheet I don't mean change them both to be the same, I mean control them seperately for each frame so they are what they are supposed to be. I would be surprised if that is not an option, because it's fairly fundamental to what the tool is trying to achieve.
(Though as it happens on these frames listed BB drop is only a few mm apart, so the crude option of making them both the same would get you very close to the right answer. Certainly much, much closer than you have been so far.)
No, not really. Having a comparison with the BB as reference is the accurate way of comparing rider positions between bikes - but only if you can use the measurements you have to properly model the bike. Lining the wheels up instead doesn't help you do that, it is in fact introducing yet another inaccuracy into the process.Indeed, it would be useful if you could see the comparison with the wheels on the same level,
Once again; if you don't understand these issues and how they relate to each other yet, you should probably avoid trying to give geometry chart based advice until you've spent more time learning about it.