It's a while since I worked with Read-Aloud but I was pretty happy with the results. It worked in Books on my Mac, on the iPad, on iPhone. I didn't encounter the sync timing you mention on the Mac. I was using a very old Mac Pro (early 2009) which is stuck forever in OS X El Capitan. I haven't tried it on my MacBook, which runs Catalina (I didn't have it when I did the Read-Aloud project).
With the epub in Kobo I had a similar experience to yours . I'll have to delve back in to see what worked and what didn't, but I recall it wasn't everything.
XPUB I haven't done much with, apart from previewing. My main focus has been optimising for epub. But XPUBs are even larger files, aren't they), than EPUBs? I could be wrong.
I'm really impressed that you're doing Android and iOS apps as well, and would love to hear more about that. I did a test iOS app with my bells-and-whistles book, but the results were disappointing. Big, big file.
Can I buy a copy of your book(s). It would be so helpful to see what others are building in Pubcoder, and exchange ideas. I can point you to my website, if you'd be interested.
Thanks for posting :)