Currently when ~~~ is inserted instead of the usual ~~~~, MediaWiki raises the missing signature flag. But ~~~ is genuinely the signature.
Possible reason: ~~~ doesn't insert timestamp.
Argument: Some users may want to implement their own timestamp format using transclusion, thus their ~~~ includes a timestamp as well, just formatted differently. Raising the flag may cause misunderstanding.
There are genuine logistical reasons why this may have been implemented. While three tildes counts as a signature for the purposes of notifications, a lot of bots, at least on enwiki, require the standard (UTC) timestamp to function right. Besides that, I'm pretty sure it would interfere with T207567 which uses regex to parse the date and decide when to load.
I could be wrong, though.
A user on enwiki was blocked over this issue a while back. I'm declining this task since there doesn't seem to be consensus that custom timestamps are valid signature options.
Anyone more experienced with this stuff than me is free to re-open it, though.