I would assume they want to factor in startup time as well as IO handling overhead - raw disk IO should be the same given programs are run in the same environment.
Tell her the truth (as I understand it you don't think she's fat), but also ask why she's asking in the first place. Offer some support if she wants to lose some weight.
I think open and honest discussion is the best approach here because now you're jus guessing what the real issue is.
It's recommended to install YunoHost on fresh, dedicated systems. It'll most likely not break anything but it's best to have backup ready. It is possible to then expose docker containers, but I'd just recommend installing Nextcloud in ynh and transfer the contents over.
The way the game drip feeds you information. I love it!