I've been hiking with a Porter as my sole pack for the last two years (for all trips, overnight to seven days out), and I personally can't see the need for any of the mods you listed. Just a few thoughts to consider, from my hiking experience:
1. Custom pockets aren't really that useful with the Porter. The attachments aren't as secure as sewn-in pockets, meaning that's what is inside tends to flop around to a mild extent. It's much better in my opinion to just use the three straps to hold whatever you need in, and the items are much more secure and locked-in that way. I do have a pair of Zimmerbuilt side pockets, and they are well-built and nice. But I rarely use them after getting a Porter stuff pocket on the front of the pack--less shifting and easier to use.
2 & 3. If you're going to be using the pack with smaller loads (which I do often), the Y-strap is really useful for compressing the load. Frankly, I have yet to find it in my way--it only takes a few seconds to buckle in--and it helps significantly in keeping things from shifting in the pack. I have no desire to hike without it, even when I don't need it for a particular trip because it is, at the very least, mildly helpful and never in the way. More often, it's even more useful than that.
4. Do what you'd like about the hipbelt pockets. I don't really care for HMG's current pocket design as you have to unzip the whole pocket to access what's inside (based on the shape of the pockets and location of the zipper). They're plenty big enough for me, and it's a minor issue. But it's also not worth getting too worked up about either way. Personal preference here.
----The only mod I would in any way advocate is to have the Ice Pack Belt put on the Porter. I have a minor variation of the Ice Pack Belt (described here), designed to allow me to use either a Granite Gear and ULA belt in addition to the HMG belt. But personally, I like the way the HMG belt carries so well, that I see no need for another company. If I were doing it over again, I'd just have the Ice Pack belt put on. I do think that it carries modestly (but noticeably) better than their standard Porter belt (for lots of reasons I won't go into here).
Other than that, I think it's an extremely well-built pack by a fantastic company.