1. The control file with the name, version and license ist something I really think is a good feature since unfortunately for quite a bit of software it is pretty difficult to find the license condition. Please make sure that the licence contains the base info like "freeware", "shareware", ... as well as the info about distribution "may be copied freely", "charge for copy may cover cost for postage and disc only", "need consent from author before passing on", "may be gotten from authors website only", "may pe put on cover discs" and the like.
2. I can understand your idea of a base installation path since it makes things easier for you. If you indeed isist on definig a path where to install the app and then setting up links or stubs: Please do let the user define that base path for the application so that e.g. I can decide where the software may sit on my disc. E.g. my root directory is pretty empty containing "!Boot", "Programs", "Data" and "Work" only. The original folders like "Apps", "Utilities", ... have been moved inside "Programs".
3. As for that installation path perhaps this might be a possible idea for a bit more flexibility: I assume that the package manager keeps a list of what it installed on the local system. If you let the user specify where an app goes it could put the location down in that list.
4. Furthermore some scanning tool to search a directory or a list of them for the installed apps for the package manager is sensible so that the user can even move an app some place else and the aforementioned database is rebuilt. (Don't scann the full harddisc since that might take a bit too long and I can't hide e.g. previous versions of some app I backed up just in case).
5. As for the links or stubs: There is the odd case where I need to go into an app directory. That is no fun with those stubs and I'm nore sure about the links since I never saw any sensible link type solution for RISC OS yet.
6. One of the things nice in RISC OS is that I as the user can decide where I want to put my apps and thus have the odd subdirectory in my folder "Programs" to get some structure to what is where - this is partially vital since we don't have that start menu where I find all the apps (o.k. there is the odd tool to address that but they need to be manually filled). Thus my applications are grouped and with Filer- or Director I have a sensible menu structure to run them.