That doesn't make much sense. When compiling atmosphere, you compile every homebrew atmosphere normally ships with.
even if theoretically something was compiler linked to libnx version, other ABI, and so on, those homebrew would be compile time linked to the atmosphere fork.
for atmosphere, the only included homebrew .nro's are the usb mtp one, daybreak (firmware upgrade/downgrader) and reboot_to_payload, all of which is compiled while compiling atmosphere
that and /atmosphere/hbl.nsp (homebrew launcher ship/trampoline) + ./hbmenu.nro (what you launch opening album) (these two are not compiled fresh during releases, but rather includes the latest versions from switchbrew)
tl:dr sounds like problem caused by something else, not my fork.