I am connecting two building together using a fiber cable. At one end is my MicroTik router, and at the other end is a QuikTrex media converter (https://www.lanshack.com/Gigabit-Media-Converters-C213). Both will be using the same SFP module. From what I understand, these devices will in fact be communicating over the fiber link using ethernet protocol. Is that correct? Are these two devices likely to be able to talk to each other?
Yes, both devices will talk ethernet and as long as modules are compatible (and supported by respective devices) things should just work.