Woo, my password finally works again. Bizarre.
Anyway, being the author of that SDA run (And I really should get more anal about people capitalizing my name properly..."EmptyEye" is the most common misspelling, though "Empty Eye" is another one. And let's not get into my cousin, who will occasionally intentionally misspell my real first name as "Mark" just to piss me off.), maybe I could lend some help in your preparing the TAS.
-The first thing that came immediately to mind as far as "What could a TAS do to save time versus my run?" was...well, using a shorter name ("Marc" is my real first name, if you're curious. Also, I know you've looked at the run already, but check out the comments as well if you haven't yet.). The second thing that came to mind, though, was skipping the R. Armor, which saves you almost a minute plus some Rupias. I grabbed it because, my run being done on a console in real-time, it was worth losing the minute to permanently double my defense and avoid constant going to the menu for Defenee, as my menu manipulation skills are rather weak.
-As others have said, definitely plan out precisely how much of everything you'll need, and grab exactly that, no more, no less (I actually went a little overboard in terms of grabbing Rupias later on).
-Pretty much everything you could think of in terms of "This would be an awesome sequence break, why didn't Emptyeye do it?" is because I did try it and it didn't work. You already saw that with skipping Pukin; the other big one I could think of would be going to the end game without going to Sabaron's room first (Scheherazade simply never appears if you do this).
-Defenee actually has nothing to do with attack power (The reason I kill Gilga's eyes in one hit is because I'm level 4); it doubles your defense power for a time. Since I imagine you can manipulate what enemies you want to appear or not, this is another reason to not get the R. Armor.
-The Eclipses seemed, from my observations, to be time-based, with the timer reseting upon entering a new chapter. Incidentally, my Chapter 4 was the hardest one to decide precisely what I was going to do route-wise (Also, if you're not using the Eclipse, you can obviously skip the magics too, saving you more time), and I ended up wasting a bit of time waiting for said Eclipse, so I'm not surprised that it didn't show up for you (As you should obviously be quicker than me).
-Tristal: Yeah, he changed classes because he had to, as he already explained.
-R. Seeds, besides turning you invisible, also let you walk on water. This may be worth looking into to see whether you can optimize overworld routes more than I did. The practical application seems pretty limited from what I found--you can only exit screens through "official" exits as it were--but give it a try anyway.
Hopefully some of that helps out.