I wanted to know if there was some switch/option that could be used upon installation to install the system on the 2 first hdd using mdadm and raid-1.
Or do we need to setup the base system first using debian*iso, then follow the post-install note ?
This is an advanced use case and it is not covered by Yunohost itself. The goal is to be easy and straightforward for most people and rely on the backup/restore system instead of hard drive redundancy.
So you should install a base debian and then install yunohost on top of it. Yunohost does not mind on what is installed.
@JimboJoe has an installation with raid + luks here Yunohost + RAID? (in french but you should get the idea )