I changed out the dome on my 5th wheel a few weeks ago as I had cracked it by leaning too heavily on an old and fragile dome. My original intention was to change only the outer dome but quickly found they were part and parcel of the same unit and mounted from the outside. I ended up changing both but the new inside one mounted from the inside and had all the trim required. I was obliged to remove the original trim on the inside so everything fit together.
If you found water inside I would be surprised that at least the edges of the hole does not show evidence of water getting into the roof material. It may not show with everything still in place but it will likely be the case. I used a wood hardener all around the edges of the plywood before putting it all back together. (Dicor roof) I replaced all screws with stainless as many of the originals were close to being rusted out completely. I was lucky to get them all out. (The hole spacing on the new dome was not the same anyway so breaking off 1 or two turned out to be a non-issue.)
Of course, having to do both more than doubled the cost with the inner being more expensive than the outer dome for matching parts from the same manufacturer. I had to internet shop in different places for each to get the best prices.