Hey,
Thanks for the nice words and I'm glad you enjoyed the game.
The Order was founded in 1119 and got disbanded in 1312. The last Grand Master was Jaques de Molay who got burned at the stake in 1314.
These are all historical facts that can be checked on Wikipedia for example.
The fiction starts after that point. They went into hiding but kept most of their ranks, habits, and so on. In those roughly 700 years they had several Grand Masters, none of them lived for an exceptionally long lifespan.
I might add the year of de Molay's death to make it clear, he's not THE previous Grand Master, just one of them (and dead for over 700 years now).
Regarding the ending: yes, you're pretty much right. There's a main plot, all main LIs have their own story arcs and they weave into the main plot at times. But they don't change the overall main story. Hard to answer without going into spoilers.
The side girls are side content and/or side characters. Mostly to add a bit of spice or fun activities, that don't fit one of the main girl's routes (at that time).
Right now, you don't need to avoid them, as all of Book 1 is considered "introduction". There will be a point when you need to decide on one girl's path and after that point, messing around with anyone else would be considered cheating.
Hope, that answers your questions. If not, feel free to get back to me.