Let's compare it to system 7 then, from the same time: still true.
WBStartup is not the same. Extensions are not programs, they are libraries. Birdie designed by a sane person would be a library with a Pref panel to control it.
Applescript in the startup programs folder.
It's not a huge hack. it's a teeny tiny one that just replaces window borders and then buggers off for a drink. Kalidoscope is from the system 7 era, replaces the entire interface, and requires no editing of weird text files.
don't forget that OS9 didn't have preemptive multitasking, and is still a decade later than OS3, also thats only ONE of the reasons for WBstartup and Startup-sequence or User-Startup.
Some time hacks or programs must be run before or after something other, also putting configurability is another reason that something is in need to run from Shell (user startup or S-S)
in Mac you Can't have parameters in the extensions you add, nor you can control the priority of the task not even the startup priority, thats why we mac technicians renamed some extensions with symbols or number before name, so to start them first, example is ATM manager.
Advanced stuff needs advanced interaction! ;-)