Yeah, it's not a real change to the rules, but it's potentially a huge change to the rules
text. Frankly, making mods to that degree is ultimately governed by a very practical issue: rejiggering all those numbers and double checking them is simply a
lot more work than anyone has signed up for. (It's already a bit bigger than I thought it would be!) So we're trying to keep this project mostly at the level of deleting material and maintaining internal consistency, rather than fully renovating it at risk of introducing even more inconsistency. Afaict, this is a first attempt at something like this, so we're approaching it with baby steps.
That said, I
really do hope this project continues on after this first "v1.0" iteration is completed, so we can start building up alternatives to the SRD as we're writing now. At that point, enterprising and energetic souls can mod the 773y out of it into something that's more robust.
Regarding feats, the short of it is that we've included all feats that come bundled with the full SRD, which includes a fair number of [general] and [metamagic] ones in the Divine and Psionics rules. The rationale is that E6 is very feat-dependent for epic advancement, so we went with a philsophy of more options to accomodate default "gestalt" games. Yes, this is the big, glaring exception to our normal rule of "SRD only". But we did it essentially for the same reason that we didn't simply axe artifacts and every monster with a high-level SLA.
If/when you find non-E6 material that has slipped through the first vetting process (eg, the feats you've mentioned), you can post the problem reports here, email the project address at e6BaselineSRD -at- gmail, or use the comment system on the site itself (the files are grouped by category, and the comment boxes are on the "category" pages). Anything goes; it's pretty informal!
And I'm going to go take a look at the ones you've mentioned and get them sorted out shortly. Thanks!