my team and I are working on a colony sim game during the godot wildjam (which started around the same time and as the same duration) 
is it fine if we participate in this one too ?

Sure why not, go ahead, it just must be an "RTS and has to run on Windows, and follow the rules as closely as possible", I will just take note your in 2 jams and I will read their rules and mitigate it for ya!, Me too I get bogged up at times and sometimes have to use same things for multiple projects in our case Jams so yes go ahead! :) Keep in mind submissions on either end may lock up your Main game file page! I was in a Jam once and it oddly included in Voting times before I can edit the main files as I thought the game jam page ripped a copy, but all it did was make a pointer to the main page and froze everything except changing how the page looks and what it says! So if theirs is unlimited edits in submissions do them 1st then mine after! Also I would love to test out the colony sim as it sounds fun! :)