I have a 5 second timelapse video, but because of the clouds passing by, my frame gets darker for 1-2 seconds. Can these be fixed by using LR + LRTL?

I thought of using more than 2 key frames and matching those scenes in Lightroom, than reloading them to LRtimelapse hitting auto transaction... Would that work?

Yes you can try that. However 5 seconds is really short.

Does it mean,

The more frames (seconds) I have, the transition become much smoother?


Thanks

Sure - normally a time lapse sequence is at least 10 seconds, so you have some room to edit, fade etc. later in post.