Issue Let's Encrypt Wildcard certificate without main domain in SAN
Currently the Let's Encrypt Wildcard requires that main domain would be hosted on the Plesk server, and pass the HTTP-01 challenge as well as DNS-01 for Let's Encrypt.
However for issue the Wildcard Let's encrypt require only DNS-01 challenge.
The HTTP-01 limits the causing the issue since not always the main domain is hosted on the same server as the subdomains.

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b.pedini commented
1 man hour job to implement + 3 man hours job to test and verify:
add an optional checkbox (like the ones for securing "www" and "webmail"), to "Force DNS-01 verification", maybe under an "Advanced features" section. -
Jan commented
Another (easier) option would be to just verify all with the DNS-01 challenge and not use HTTP-01 at all as there are different occasians where HTTP challenges are problematic.