That's unlikely. Worst case: examine where the package will put its files, and prep your system with symbolic links to directories residing on a file system on the other disk(s).
But that raises the question: why are your file systems sensitive to disk drives? Use a layer (or more) of indirection through LVM and RAID so to make the drive placement opaque and robust.
> why are your file systems sensitive to disk drives?
A couple of systems I have at home have a 16GB primary disk, so it is useful to be able to put things on an external disk. I have yet to see any package manager that can actually handle that.
> Use a layer (or more) of indirection through LVM and RAID...
Yeah, that's a great idea, just introduce more complication and abstraction to make up for a shortcoming in how Linux developers think about applications.
Or, just have your programs be self contained in a single file or folder and put them wherever it makes sense.
Also can't install to separate disks.