I do not agree with your interpretation of the guidelines, but I actually did not follow them when I filed my I-130/I-485/I-765 (I had not read those guidelines when I filed). Here is what I think the guidelines tell you: keep I-130 and I-485/I-765 separate. Attach one check to I-130 and attach two checks to I-485 (one for I-485 + FP and one for I-765).
The guidelines do not explicitly state what to do in case of concurrent filing. Another plausible interpretation would be that I-130 is "supporting documentation" for I-485, in which case you would attached all three checks to your I-485 (paper clip in upper left corner). I think it makes sense to keep the two separate because I-130 is filed by petitioner and I-485/I-765 by immigrant, but probably does not make much of a difference.
The way I did it was to attach a single check to each of the forms that required fees. In other words, one check for I-130, one for I-485, and one for I-765. USCIS accepted my applications without problems. It really does not matter that much so long as you include everything in a reasonable order. The most important thing is what you include, not how you include it. Remember that these are guidelines, not requirements. They will not send back your application just because you used an unconventional ordering. Just relax a bit and use common sense. Attach things where it makes sense and so that nothing gets lost. The cover letter helps them locate all the information.
