For an 18th century orchestra of the sort Bach was writing for, the instruments were made to play together. Intonation of baroque oboes and classical clarinets was reasonably accurate, and everything else could tune to them just as they do today. You would very rarely have an instrument from out of town joining in the band.

The tricky one was organs - retuning a large organ is something you do every few decades, not when some hot-shot trumpeter wants a gig. Often the organ would be set in some tuning that hadn't been used by the local orchestra for decades. So the result could, um, interesting. This article shows how Bach was sometimes driven to arrangements where the strings played in the organ's pitch and the recorders had to either be made in weird pitches or play in bizarre transpositions to fit in:

Tarasov on Bach cantatas featuring the recorder

(Warning: that made my brain hurt).