Two companies one tenant, advice welcome

I think it’s always going to be a little messy too.  For the mailboxes, if it didn’t matter what the sending domain was, you can always set up the second company as an alias on the primary mailbox.  The downside is that you can’t send from an alias, so any outgoing emails would always come from company 1.

I think if you have to be able to send from both company 1 and company 2, I would go with your method of just creating a second users for company 2 and then purchasing an Exchange only license for them.  In effect I have this in my tenant only it’s a primary account for my company and a secondary account (with an exchange only licenses) for one of my personal email address/domains.  Since they are in the same tenant, you can open the secondary mailbox from within OWA (while signed into the first) if you set up all the permissions correctly, or you just sent up both accounts in Outlook on the desktop (or mobile).

Just my two cents, but I think you have a couple different ways you could do it without any one choice being inherintly better, they all have various advantages/disadvantes.