Gonna use the summary.
1. Depends on context and is hence case-by-case
For lots of fictions physical size is a meaningless indicator as their power system isn't structured around that but more qualitative ideas.
2. I assume I can skip these. Disagree in any case.
3. Plot relevance and ordinals seem like meaningless indicators of scale. Just containing more stuff that countable infinite universes doesn't IMO suffice to reach Low 1-C. A non-significantly large 5th dimension also can contain more stuff, after all.
4. We currently mostly tier being beyond any logical system as all being the same rank (i.e. ZFC rank). That's a practice I don't like either, although I have different opinion on how I would prefer things to be ranked. Conceptual Transcendance as a tiering tool is fine in my book, though. Just that it should not all end up in a "transcends logical system" tier but rather as evaluated relative to what is in the fiction.
5. aleph_4 for Tier 0 would be too low, as that would be one aleph for infinite levels of infinity. It would make more sense to say: Below 1-A is infinite dimension stuff, 1-A starts as Aleph_2, High 1-A at Aleph_omega and tier 0 at Aleph_2*omega or something. That way an infinite hierarchy of levels of infinity is 1-to-1 matched by an infinite hierarchy of alephs. But any revisions of such nature can't be done in a middle of some thread like this and personally I don't think it's the right time.
6. No. Not just Durability but also AP and Speed ratings vary to some degree based on amount of damage done and stuff. Such unquantifiable factors are in all our stats. Ideally we should always give a range of stats, but that is just unrealistic in terms of effort. Our rating systems are simplified in many ways and assigning each character one rating for the consistent peak feats is one such aspects. I don't think it should be changed.
7. Honestly, don't think we need a mathematical example. Only suits the mathematical verses anyway, nothing else cares. Of course, if there is some good one we could add it somewhere, but it is a complicated debate and I don't care for it.
So... I guess put me down as disagree for 1-6 and neutral on 7.