FMOD Studio always re-encodes source assets when building banks, so this is less a question of how the audio will be in your game, and more a question of what works best for your FMOD Studio workflow. We generally recommend using the highest quality source assets possible, so if it’s easier for your workflow and you have the space for it, using your WAV masters is probably marginally more “optimal” than using OGG re-encodes, though at that samplerate and bitrate the difference should be negligible.
The only circumstance where I might be concerned about the cleanliness of loops is when encoding from specific source formats that make use of padding or a set frame size, notably mp3. Otherwise, compression during bank building shouldn’t affect looping behavior. You can read more about this issue in one of my responses here: MP3 loops with an audible gap, the equivalent WAV doesn't - #3 by Leah_FMOD
As for the reverb tail case you mentioned, while it’s possible to crossfade between audio to make transitions like that more smooth, removing actual content from an asset isn’t something that Studio is built to handle. You’d want to render out separate assets for the loop and intro audio so that the reverb tail isn’t present.