Selfhosted SSL cert issue

Hi, I’m hosting mastodon for personal use on subdomain.domain.tld — it has a valid ssl cert. The issue is that when I set the vanity server name to domain.tld (no subdomain) and create a Let’s Encrypt cert for domain.tld. The namecheap ssl cert checker says that the Hostname doesn’t match the Common Name or/and the SANs.

I have domain.tld redirect via an Alias record to my Synology server (just like the subdomain) but for some reason it’s fine on the subdomain but not for the root domain.

Any one have any experience with this? TIA.