Greg:
It's probably only the result of some anal-retentive people.
Unless the silicone mat is really thick (they usually aren't), you won't lose any significant power. Here's the thing though: is the mat transparent enough that you can see where the burners are, so you can properly position the pots and pans on? (A pot that is not centered on the burner will only receive power in the parts that are on the burner.)
Smooth top cooktops are easy to keep clean, and induction cooktops are even easier, just wiping with the proper cleaning solution does it, there is no need for "protection". In fact, if sugar, salt etc get trapped under the mat they can scratch the surface over time much more easily than if the surface gets wiped every time it's used.
Maybe someone put the mat down because the pots and pans slide really easily on smooth tops?
The other "risk" I can see when one has newspaper, parchment paper or silicone mats on induction stovetops is that if the temperature on the (particularly empty) pots exceeds the safe temperature for the paper or silicone, it can either melt or catch fire. The mess to clean will be much bigger than if you had just the pot on the glass-ceramic surface.
The thing to remember is that glass-ceramic smooth tops are not exactly "delicate". Any material in the glass, ceramic or glass-ceramic space exists in a weird balance and you can have either something that is extremely mechanically resistant (gorilla glass), or resistant to extreme thermal shock (ceran smooth tops) or resistant to chemical attacks. No material is perfect.
Ceran (and other smooth tops made of similar materials) are extremely resistant to thermal shocks, relatively resistant to mechanical shocks but their resistance to some chemical attacks (in this case sugars and starches) is on the low side and if the temperature is high enough, any spills (tomato sauce, caramel etc) can either pit and/or fuse to the surface. Another source of problems is grains of salt, sugar, sand etc on the surface might scratch the surface, particularly if people have a habit of sliding the pan back-and-forth on the smooth top instead of stirring the contents.
But my question is that it's weird for people, particularly in churches, to be worried about the appearance of their cooktop to that point. Did they have a standard smooth top (radiant heat) that somehow had a short life due to careless users and that's what made them decide on induction?
Please keep us posted -- from my perspective it's not worth having the fight to force them to remove the mat, but it's not worth the expense of buying a mat to use for that either. I'm just curious what is the history of the previous cooktop if any and the stories they'll tell. Given that induction cooktops operate at a *much* lower temperature than radiant cooktops, I would expect a much simpler cleanup and much improved service life.
Cheers,
-- Paulo.