Creating certificates with a bunch of SAN entries is definitely possible but a programming nightmare to manage on my end. It would be easier to register a few more domains such as example.com, example2.com etc and have the LE certificates issued under those. In a perfect world, strongswan would support wildcard certificates that I could use but unfortunately they don’t and probably won’t due to their own reasonings.
Would you happen to have a link for the rate limit increase? The URL I found seemed to be for people who are above the 500 certificate mark which I a not (yet). I can deal with with the limit of 20 per week but the upper limit on how many can be issued against a specific domain is what is killing me.