Perfect we are in agreement over this little frame data exercise that Roy does get a decent frame advantage out of this. Enough that he cannot simply be tanked and retaliated against at a 50% threshold. At lower percents lower than 50% I readily agree he can be tanked and retaliated against. How much lower I am not sure. 40% is 16 frames hitstun for samus though.
Alright, the next thing you brought up is that after Samus gets hit she can easily double jump, air dodge, or bomb. These are really the only things she can accomplish other than trying an aerial. Which I think we can agree now that Roy can cover this option of attacking if Samus tries to attack directly.
-Double jump depends. If we are on FD, then Samus stalls her situation of being in the air . Still has to come back down again and Roy can have the ability to cover the landing again. He merely moves to another location of the stage. If she double jumps to another platform, then yes, Samus gets away.
-Air dodge. Simply from experience many times on Marth and other characters in general an air dodge can be punished even if you whiff on the I-frames. It depends upon how low you go to the ground before doing it. The longer you wait the less you can actually react to a character trying to hit you. I believe Roy can cover this option as well.
-Bomb is a stalling method like 2nd jump, but a much lower trajectory. There is still lag from putting out a bomb as well. This too I think Roy can cover.
My point to this is that other than 2nd jump to a platform Roy can have the ability to cover several air options Samus has following the hit of a weak Uair at low percents. Therefore, he maintains an advantaged position even after hitting Samus with the weak part of Uair. So, it does not seem to far fetched to me to believe this scenario might be duplicated on other hits from Grab, Dtilt, etc. until Samus is at a higher enough percent to routinely get knocked offstage into edgeguarding. Roy has to play well and keep denying these options to gain control of the stage.
It will be difficult to do this, but the fact is that Roy can respond to options and this is why I see him being able to maintain advantages. The rest would be having some pilot that is good enough to pull this off without messing up and 14(?) years into the meta players are getting pretty good.
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Now, since the only option Roy cannot cover is 2nd jump to a platform I will tackle what you mentioned about top platforms.
The first thing to take note of is that top platforms threaten nothing for Roy on the ground. If he has the stock/% advantage he has little reason to go up there and merely wait for many character to try to get back down. Should he lose such an advantage he does not have to fully commit to engaging them on the top platforms and stay grounded. If the opponent is very adamant about staying up there and only 2 minutes are left on the clock and Roy is down in stock or % lead he finally should start to make shots at the people up there. Although, I am certain most players would have gotten off the top platform against Roy by this time.
An advantage Roy has with being a fast faller and disjoint is he can try taking shots at people through the platform and get down to the ground before many of them have the ability to come and punish him for doing it. While he does not get any lasting advantage out of it any hits will tick up %. But yes, this is about the extent of what I think Roy can with platform play unless he manages to land strong hits and force tech chasing situations on platforms. Or get between people and the platform.
I am not going to say Roy is perfect and should be like Marth reaching like top 3. I am thinking that he might have the ability to rise a bit more to at or below the Links. Yoshi seems to be above the links as a character anyway.