You're going to come up against more of this yet in the future, (store audio in its own folder), and I THINK I have a solution I haven't been able to test yet. It SHOULD apply to projects, VSTs, bundles, etc.
It is probably going to be time consuming, but, maybe more so early on, less as I see what's what.
Plan is to get a piece of paper and a pen, copy and rename one dll, while documenting old and new names, create a new folder, put the renamed dll in the new folder, have Sonar rescan, and see if the newly named dll works as it should when called up.
Same for projects and bundles.
If all goes well, I will end up with dlls and samples on the respective PC, projects and bundles on a local cloud drive, in a file system with nested directories, backed up to the house file server regularly, which in turn is backed up to offsite media, with attendant audio files invisible under the respective project folder in a subdirectory of their own.
As it stands right now, I've allowed Sonar and the plugins to install as they wished, and have 32 bit dlls in the 64 bit folder, vice versa, and projects in their own directories, but the attendant audio junkpiled in folders all visible in the Project main directory, along with the nested Project subdirectories.
Over decades, I've found its usually best to accept the defaults on installation routines, but every rule has its exception and this looks like one of them.