i share your feelings.
i started perhaps 19 months ago with a new book using what was up to date software at that time. my main tools are iba and keynote, mac os and iOS and ibooks of course. about six months after i started, new versions of the software came out. the newer iba's were ok until the new keynote came out. a simple drop of a new keynote into a keynote widget did not work, and the best i got from apple support was that they could not recreate it and it must be something with my data. i couldn't waste time with this so i decided to keep developing with the older software. around the 15th month timeframe and perhaps 90% of the work done, i came to realize that it was a losing strategy to send my book to apple based on the old software, so i updated everything. it was a disaster for me.
1. the first problem i noticed was the problem i had described above about dropping the keynote documents into the keynote widgets. lucky for me i stumpled upon a workaround. i mentioned this in passing to apple support while discussing another problem and the level 2 support guy (who was very good) picked my brain about it before we finished. contrast this to my previous experience where i never got past level 1 support. i sent an email describing this problem to apple support and expressed my disappointment on the job they had done. i got a nice letter in return acknowledging that perhaps they could have done better.
2. keynote movies and audio would no longer loop (i documented this on this forum). this was a serious problem for me. i got a workaround from apple. i hope they fix it.
3. after an iOS update, i couldn't use preview to an iPad (i documented this on this forum). i found an alternative method to preview on an iPad, thanks to a contributor on this forum.
4. and this portrait issue, which is not a problem but a feature change. you can read my comments above to which i now add:
a. perhaps there is a good reason why they did this but cannot tell us and that i cannot determine.
b. but the really good news is that i came to realize that the portrait view of my landscape book is terrible looking and useless. no customer would look at it in that orientation for a long time. they would rotate the iPad. if that is your only issue, count your blessings. it's not going to matter to your customers and will not impact your timeline to bring your book to market. (got me thinking about a monitor in portrait mode and reading a landscape book on a mac. wonder how that looks?)
i wasted all of last july reestablishing a workflow to get my book done.
the inconvenient truth is that we you want to be in this business, you have to factor in updating software. there is no escape around it.
i am at a point where i can get my book into the bookstore perhaps by the end of september. i am torn about doing the updates to iOS 9, iTunes and any of my other critical software that can impact this book. but i feel compelled to upload my book produced with the new software. what i really need is a test computer where i can test out new releases of software before i put them into the main production computer. now, why didn't i think of that before, a test computer and a test iPad for new software. can a trip to the apple store be in my close future? if everybody does this, apple stands to make a lot of money.
Disclosure: I own Apple shares.