They have not a spam filter, they are using greylisting, that it is a completely different thing. All legitimate mail systems are able to pass-through, even the validation one from SE, so there is nothing to fix. The only thing is that the first email from anyone, will take some time before reach inbox, because greylisting process.

After initial validation, any subsequent emails from same "from" address and same IP, will pass through immediately without delay. It means, when today I will try again to validate my one time password, the validation email come to me as soon as it is sent, provided SE uses the same mail merver, or else I get delays again, because IP of sender has changed.

I don't think making the validation email expire just after 2 hours instead of one, breaks any security.