Regarding package specific customization, check out this proposal on the table for 4.7:
https://openacs.org/forums/message-view?message_id=63062
Regarding the original bug, I believe this has to do with "oacs_root/tcl/zz-postload.tcl" only loading query files within the "oacs_root/www" and "oacs_root/tcl" directories. The hack is to change this line in "zz-postload.tcl":
set dirs {www tcl}
to:
set dirs {www tcl add_your_dirs_here}
The REAL answer is to probably recursively descend through the oacs_root/www hierarchy looking for and loading *.xql files.