ummmmm....I think you may have created a serious leak waiting to happen that'll not be covered under warranty. I got into this Raptor after 4 GM trucks - so I did alot of research on Ford F150s/Raptors beforehand to see what the common issues were. Well - this dual pane sunroof has been a problem for years, mostly earlier 13-15 models it seems - but newer ones also have their issues. For me - I needed a SCREW, and the vast majority of SCREW Raptors & well optioned F150's in general have this option, so I figured I'd go w/ it & get a 100k extended warranty just in case.
For starters, the warranty - extended or otherwise - doesn't cover "wear on weatherstripping" or something to that effect, so if you start developing a rattle or leak w/ your sunroof & then screw around w/ silicone I'm fairly certain if they notice it they will void any warranty related to the sunroof.
From what I have found there are 3 problem areas w/ the sunroof.
First - the drainage tubes can get clogged over time backing up & depending on what angle your truck is setting + how heavy the rainfall/carwash may be would determine when/if the drainage tubes become overburdened & can't handle the flow- so probably worth checking once a year & cleaning by running a pipe cleaner or something through them. They could also be pinched/installed improperly or become disconnected even when new from the factory - not that common, but has happened.
second - the middle seam of rubber to rubber where the movable sunroof pane meets the fixed one is a problem area on 2 fronts. When the truck gets wet then dries back out there can be a some "stickiness" between the 2 rubber seams where water deposits have dried - when you open the sunroof w/ the slide function & it drops down it can REALLY break apart from the fixed panel HARD & this can cause the sunroof to become misaligned and/or break tabs on the rails (which are cheap plastic & there are upgraded replacements available) - I noticed this even on a brand new one on a test drive, always venting the roof first (popping up) before sliding it back I think helps prevent the rougher/yank movement - seems to "release" easier after getting "sticky dry" popping up than dropping down. Every few thousand miles as regular maintenance should pop open the vent stand on either side of the truck wipe down the rubber seals w/ wet rag then apply thin layer of "krytox" silicone paste - there are other brands/types out there that may be cheaper, but that's what Ford recommends so that's what I'll be using.
Third/lastly - sorta mentioned above, but in addition to the plastic hinge type pieces cracking, breaking off pieces into the rails, causing the sunroof panels to get stuck in a position and/or become misaligned so they don't seal correctly, causing leaks and/or malfunction. Additionally, there are a number of small metal tabs just under the glass running along the length of the whole assembly - kinda rectangular in shape w/ tapered ends each about 2-3" long w/ 2 screws attaching them. There can start to be some play between the fixed rail & where these tabs attach, when going over bumpy surfaces particularly off angle side-to-side you hear a rattle & thats the rail or whatever tapping against the back side of these metal tabs. Super easy simple fix was to stick some self adhesive rubber weatherstripping to fill that gap in & eliminate the sound.
Hate to drop that on ya, but without pics based on what you're saying you did I think that may have been a mistake.