The rubber grommets will attract and hold water, through capillary attraction. If there isn't sufficient corrosion protection, there can be corrosion.
Because grommets are soft, and can move, the only thing that would work well with a rubber grommet, would be to paint it first. Or, use some type of coating, that will dry hard like paint. This could be done with a brush in this case. Keep in mind that paint does not like to cover sharp edges, so, it may take some effort, and several coats. As, well as allowing a good amount of time for drying, prior to installing the grommets.
I do not recommend silicone for sealing a grommet. Or, much else, actually. (Aquariums, and bathtubs excepted). However, it would be better than nothing. And, may be enough in this application.
Silicone calk is not ideal on bare metal. I have never seen it used by any automotive manufacturer for a sealant, or corrosion protection.
There are sealants that don't harden at all, like butyl. which would be better. But they are not always easy for the general public to get. Or, inexpensive.
This gutter sealant, is inexpensive, and sticks to bare metal, as well as painted surfaces extremely well:
Shop OSI Gutter Sealant at Lowes.com It is not ideal, but would be a superior choice over silicone. It is very handy to have around the house, once you try it.
I have considerable experience, and training, and certifications in auto body repair, and painting.
