Since there are more and more jailbreaks being created by hobbyists (rather than professional teams), each with their own respective quirks, you may have to change the behavior of your tweak / packaging depending on the jailbreak installed on the user's device.
None of this advice is foolproof but it's worth taking into consideration.
Electra (11.1.2)
/.electra_installed
in the filesystem.
Electra (11.3.1)
/.electra_installed
in the filesystem.
th0r
/.bootstrapped_Th0r
in the filesystem.
unc0ver
/.installed_unc0ver
in the filesystem.