For context, how long ago / which version was it that you have used Yunohost last time?
I may misunderstand your question, but if you now install Yunohost, I think your concerns may be addressed.
Mail can be enabled/disabled on a per-domain basis. This is about public facing mail services; housekeeping mail (cron, diagnosis, etc) are sent to users belonging to the admin group.
So, if you like to run Yunohost services at yuhohost.domain.tld, but have another server deal with mail for domain.tld, you turn off mail for the domain yunohost.domain.tld.
I have some yunohosts that run at yunohost1.domain.tld or at yunohost2.domain.tld, and also a yunohost that serves yunohost3.domain.tld and domain.tld, as well as domain2.tld.
There is a similar thread, my understanding is that in that case,
- a VPS running at
yunohost.domain.tldacts as mailserver for - a homeserver running at
domain.tld;
@samuel-ynh added domain.tld to his VPS as well as having it configured at his homeserver, but selectively set DNS records (only MX, to not disturb DNS for his homeserver). This way, all functionality provided by having domain.tld configured, such as mailbox and alias management, is available at the VPS, while the actual server that runs the domain has nothing to do with mail handling. Some tweaks are needed to have this running smoothly, see his helpful post for details.