The only advantage is that libraries that are likely to be used by many programs aren't duplicated throughout the system, but instead stored in one place and as one version.
The vast majority of B3D userlibs are custom wrappers that won't work with any other applications, so there's no real reason for them to be visible to the rest of the system.
If your program does rely on a standard version of a common utility, it's probably better to flag it as required, and prompt the user to obtain it separately for themselves if they haven't got it already. If it's not common enough that you wouldn't feel happy telling someone they should have it installed, it doesn't fit in this category and you should package it with the main program.
Oh, and something else: you (as an application designer) should never be writing to a user's system folders anyway.
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