How to seal up penetration after thermocouple replacement

[Freestanding]

I have a Majestic dvrt36. The thermocouple was physically damaged, so I replaced it. Now how do I seal up the penetration in the bottom of the firebox where the pilot assembly stuff passes through?

Note that it was not sealed when I replaced the thermocouple. Most of the sealant had already been removed, presumably during some past repair. There were only a couple globs of orange sealant still clinging to the wires. So I'm hoping to learn:

1) Specifically, what product should I use? Looks a lot like Permatex high temp RTV that I would get at the auto parts store. Ideally I'd use what's already there since I'll likely be applying some fresh sealant over existing sealant and I want them to be compatible with each other and stick to each other. Also critical: I can't screw this up and use the wrong product and have something that smells (understanding that some smell is expected upon initial heating/drying/curing).

2) What exactly is the best method to glob up the penetration with the sealant? I guess I really just need to glob it in there from the underside.

3) From the underside you can see a lot of sealant. It looks like there is actually a removable square of metal as indicated by the screw. Is all that sealant just to seal the perimeter of the removable square? Why would that square be removable?

4) Why would someone have removed the sealant and not replaced it?!

5) Anything else I should know or things I might have missed?

Thanks in advance! This fireplace and my freestanding Lopi Berkshire are the primary heat sources in my 130 year old house that we just moved into. And both have been neglected. Just want to get them back in good shape, efficient, and safe.

 

[DAKSY]

Looks to be RTV. That was used by many manufacturers to seal the pilot assembly in the past,
but now small silicone grommets are used to plug the holes.
If you can get a tube of high temp RTV, it should work.
You just have to get the end of the nozzle as close to the
hole as you possibly can & liberally "goob" (technical term)
as much as you can in there. A small piece of wood,
like a popsicle stick can be used to spread it evenly...

 

[Freestanding]

Ah, see I would have globbed where I needed to goob.

K, I already have some Permatex High-Temp Red RTV Silicone Gasket Maker (which is actually orange) so I'll use that.

I actually have decent clearance from underneath, so I'll just try to remove a bit more of the existing sealant that's in the region of the penetration, then I'll goob the Permatex in there.

Thanks!