A method of selecting which account you’d like the money to be taken from if you have more than one Monzo account makes sense. Having to remember to go into your Monzo app and make sure the correct account is showing before clicking the monzo.me link is definitely not a nice UX.
There was a similar problem with Bill Splits not going to Joint accounts which was fixed:
This sounds like the sort of thing @robinb’s “core app” team might have a go at fixing at some point.