Sorry for the confusion
No, I was referring to the ones in the 2 L & R Boot, (Trunk), Wells.
The ones you are describing in the forward Boot, (Trunk), are not drains they are just Grommets, they seal off the Cavity in the Rearward Body Crossmember, just above the Ally Rear Beam / Suspension Cross-Member.
I've just looked at my own W220 on my lift, and it doesn't appear to have any holes underneath the Car in this Cross-Member, so yes it will fill with Water, but I haven't a clue how that is getting water in it, maybe that leaky Sun Roof Frame is allowing water ingress via the rear 'C' Pillars
What your Mechanic is actually saying is that it will be quite involved to fix rot in a Sunroof Frame, and it requires removal of Headlining etc etc to effect a decent repair via Welding, Paintwork etc etc, it is a job for a real good Body Shop
However, if you are serious about your Cars, like I am, it needs doing