Hello there... I have to say that I am a convert to embedded Mac libraries, for a number of reasons....
1) Mac Users chose a Mac because they are easy to use. They expect to double click a program and it to run. If it doesn't, clearly it is the fault of the programmer. Not theirs because they forgot to install something else. [Even worse is when you suggest they compile something.] I am of the same opinion, I love my Mac because usually I only have to dive beneath the hood when
I want to.
2) Because including the SDL framework merely puts a copy into the internal Frameworks folder and embedded can easly be made unembedded if someone wants to make it work with a system copy. The chances are greater that someone who is going to want to do that can understand remove instructions than that a true novice will understand how to add it.
3) The libraries are small compared to data / library files.
4) You can always produce embedded and non-embedded Versions (if you use the Apple dev tools you can easly compile both in a single pbxbuild instruction).
5) When Battle For Wesnoth had only a non-embedded Version there were lots and lots of Queries about "it won't launch". Once there was an embedded Version this vanished. Part of the problem is that the app won't run and say "can't find SDL"... it just won't run.
6) The official distribution can include a copy of SDL which is definitely compatible with the build.
All in all the best option is the dual embedded and non-embedded Versions, with the obvious choice being embedded and instructions in the readme on how to remove the embedded library.
By the way, I would suggest for the same reasons, that a fix is made to the windowed mode on OSX even if the inverted cursor co-ordinates are SDL's fault.
Dominions II is a superb game, so let it shine