I can elaborate on each of those examples
1) Those are each a separate bus trip, as they are school trips that serve students. I'd assume for the B74 it's to bring students from Mark Twain to the Coney Island Subway Station on school days only.
2) Those are similar trips, but they aren't the same internally in MTA. Internally, school open and school closed schedules are completely different, so they may look the same to the average commuter or get someone confused looking at like like why does this exist, but internally, it's a different story. Same can be explained for point 3 you maid.
To answer your question, the most reliable way is to make the schedule be based off of day, not whether or not it's a weekday or not. Remember, not all routes are created equal (example:
B6 has a different schedule on weekdays, depending on whether school is open or not, as well as the
B9). GTFS normally provides a "calendar_dates.txt" file to exclude school open schedules from being displayed on days that school is closed and vice versa. It looks something like what I will show below (this is a part of the current GTFS for Brooklyn)
service_id,date,exception_type
EN_B6-Sunday,20260525,1
EN_B6-Weekday-SDon,20260525,2
EN_B6-Weekday-SDon,20260527,2
EN_B6-Weekday-SDon,20260604,2
EN_B6-Weekday-SDon,20260619,2
EN_B6-Weekday,20260528,2
EN_B6-Weekday,20260529,2
EN_B6-Weekday,20260601,2
EN_B6-Weekday,20260602,2
EN_B6-Weekday,20260603,2
EN_B6-Weekday,20260605,2
EN_B6-Weekday,20260608,2
EN_B6-Weekday,20260609,2
EN_B6-Weekday,20260610,2
EN_B6-Weekday,20260611,2
EN_B6-Weekday,20260612,2
EN_B6-Weekday,20260615,2
EN_B6-Weekday,20260616,2
EN_B6-Weekday,20260617,2
EN_B6-Weekday,20260618,2