It looks like it was a bug - planes beyond the first didn't appear and prayer boats didn't disappear as quests were completed. But! I replayed, and didn't experience the same problem! On my second playthrough, the new planes were really obvious (although I was looking out for them, after all the advice I've had here.)
In case it helps with troubleshooting, the homeless mage was the first person I spoke to in the buggy playthrough, but after speaking to him, I went off and helped a couple of other people before finding out how to squatbreak and opening the building. This might (??!?) have prompted some kind of flag setting error (maybe?! guessing!), as his box and sign didn't disappear, his room didn't get signposted as Heresy Press as time went on, and so on.
Ah okay - sorry about that! Thanks a lot for all the detail about how it happened. I'll do my best to track down the bug and fix it!
I'm having a similar problem, the first plane didn't trigger until I got reeeeeally close to it (I spent ages wondering why I couldn't move on and came back to the page to see if anyone had an answer - which is the only reason I tried to get really close to the plane, because i'd already tried to itneract with it heaps of times but I was clearly too far away) and after that nothing seems to be appearing or reacting. I'll have another go sometime (I don't really feel like replaying through it all again right now) and hopefully it was just a one-off bug, but it definitely happened to me too!