If I make uniData as a package. When developing SideNote.lpr and I need to edit something on uniData, I have to open the package, edit and compile it. And then reopen SideNote.lpr again to continue developing.
If you open and edit the file (even if you do not open the package), then Lazarus will still recompile the file (and all packages that depend on it).
That is, unless the "files not recompiled issue" stretches into that area too.
If that issue does affect packages, then its harder to fix, as the ppu will be in the package dir....
If you want to change debug info, or other compile options for the package => you can do that from the project, via "additions and overrides". And that will work for build-modes too.
However: Using packages or not: The other problem at hand should in either case not happen....