The only thing I can think of is that AWS Certificate Manager only validates by email addresses which can be problematic if you don't have MX records or don't have control over it(Maybe a large organization where the people who do control those email addresses won't click simple verification links)
It seems a bit inconsistent as to when it will use the email on the whois record for the validation too. For some subdomains I try it will allow validation using the whois address, other times it's just the common aliases@sub.domain.com(which requires an mx record) So I guess if you're nesting deeper than one subdomain(e.g. abc.def.example.com) then maybe it'd be easier to get letsencrypt set up than try to get mx records for abc.def.example.com.
Shameless Plug/Disclaimer: I had been working on a tool to make it dead simple to use Lets-Encrypt certificates for CloudFront/ELBs and handled autorenewal via Lambda. I'm not sure there is any use for this now that this exists though.