I'm guessing lab texts from successful experiments...
I am thinking the Mercurians probably had some sort of magical theory, that Bonisagus was aware of.
Look at Flambeau, who probably had the second highest magica theory amongst the Founders. According to HoH:S, Flambeau was illiterate, yet worked out how to invent new spells, with bonuses from knowing similar spells. This was before meeting Bonisagus. And at some point he made a fist sized fire opal into his Talisman. Think of the magic theory score he had to have in order to open it for enchantment in a sngle season.
As for a "Join or Die" rebellion, remember that prior to OoH all Gifted wizards distrusted each other, so would naturally avoid "joining" this unknown group called the Order of Hermes, thinking the OoH emissary was trying to rob and/or kill them.
However, once joined they had equal rights, lots of advantages (social opportunities, Parma, new spells, etc) including Oath guaranteed safety and security. There is a distinct lack of an oppressed class ready to make common cause to revolt against their oppressors.
Did Jerbiton's original League of Thebes, arguably as big as the original Order and reasonable co-operative and organised, resist joining?
Pretty sure you could find such a class amongst the assimilated wizards. After all the Ordo Miscellania certainly resisted joining and did so under duress. I'm sure that, especially early on, the idea of "thanks for the Parma Magica, not please leave us alone" would have been fairly widespread.
Perhaps I misread the canon history, but where was the resitance and duress?
The hedge wizards that would become the Ordo Miscellanea were resisting Dav'nalleus' oppression.
Later Pralix raised them in opposition against the OoH, as part of her Tytalan philosophy, until diplomacy won through.
The Hermetic Oath can be read to say you are left alone to do your own thing so long as you don't do stuff to endanger your fellow Oath takers, as they do their own thing. The existance of so many different traditions in Ex Miscellanea suggests they have effectively been left alone since joining under Pralix's direction.
That was evidently described more precisely in HoH:S.
But there is also the old saying Die Nürnberger hängen keinen – sie hätten ihn denn zuvor!. Finding magi used to expect trouble from any other magi that find them - due to lack of Parma and resulting lack of trust - was certainly difficult.
Sort of. Most of the Greek wizards weren't much interested in joining. This lasted until Tremere and his followers started raiding for vis and other magical resources. At that point joining the Order so they would get legal protection from these attacks suddenly seemed like a much better idea.
When the OoH tried to expand into the British Isles they met with opposition from many of the traditions there, organized by The Spider. Pralix allied herself with wizards from other traditions and waged war against The Spider and his followers.
Those who had resisted joining were for the most part killed during the war, with the survivors going into hiding. The Ordo Miscellania was formed from those who had been allied with Pralix.
"Thanks for the Parma, now leave us alone" is a perfectly acceptable opinion to have.
Guernicus and most of his followers were of the opinion that "if a magus minded his own business, kept to his own property and caused no trouble to others, the Order should leave him be"