I have a few domains that are using cloudflare my actual domain where mail is hosted is using glue records and I hope to keep it that way. But can I use cloudflare for some of the domains that only have a mail alias?
Registrar, DNS, CDS?
For? To receive email via MiaB?
The registrar is irrelevant and the DNS provider is also irrelevant. CDN has nothing whatsoever to do with email, so that is super irrelevant.
So that said, no matter who you bought your domain name from or no matter who hosts your DNS, Mail-in-a-Box can provide email service.
If I am interpreting your post correctly, you have a domain which hosts email - and you have decided to use that domain for the name server as well. Which is how MiaB is designed to work. MiaB can host email for any domain … there is no requirement to have glue records for any other domain other than the one hosting MiaB.
What you need to do is to change the MX record for each additional domain whose email you want to host to point at the hostname of your MiaB. You will also need to enter the DNS records shown on the External DNS page of MiaB to wherever the domain’s DNS is hosted. Alternatively, you can host the DNS for those domains on the MiaB. If you make that choice, you want to change the nameservers at the domain registrar to ns1 and ns2 at your MiaB’s hostname. Although, personally that is not the preferred method (especially if you host websites) – you are better off to host DNS for the other domains elsewhere as MiaB could be a single point of failure (highly unlikely though).