With my original 3DS I gave up on keeping it at 4.5 since at the time I could not afford to buy a Gateway. (this was long before the Ultra 3.0 release). So I tried to update from 4.x (I forget the exact 4.0 firmware it was on, but it was in the 4.x range) to 8.x or whatever the latest firmware was at the time.
The update failed near the end due to a generic error. Not sure what happened. But the setting menu no longer started up, so some firmware titles were updated to new ones that used newer encryption, but the firmware wasn't updated to the point where it actually initialized the new keys correctly.
I didn't know about the safe mode option at the time, so I used my Pokemon X game (and I know for a fact that the FW I partially updated to was newer then 6.x) and had that update my firmware. It seemed to work perfectly fine. As far as I can tell the console was updated to 6.x using the game and setting menu worked at the time. I'm pretty sure 8.x+ system settings menu would not have booted in 6.x either. But it did, so that means it must have downgraded it? Or I might have had some frankenstein system where some titles were newer they they should be for that firmware version. Either way, my second attempt to update via internet worked and it updated to the firmware version I was intending to update it to.
No, there is nothing specific at all. It literally doesn't matter which FW you choose.
There's some spiderhax homebrew like RegionFree that only works in the 9.x range.
From what I've heard newer revisions of the Super Smash Bros cart has the 9.2 update. Majora's Mask comes with the 9.0 update I believe.
Not sure if the system update menu follows the same rules. Usually DevMan won't install CIA/Titles that are older then what they are replacing. Perhaps System Update ignores this when updating a system that had an interrupted update. For the sake of having a functional console I would think. Nintendo is not in the business of creating bricks believe it or not.
The exploit might not have been patched yet. But there is a large discrepancy with browser version vs what 4.x normally has. I don't think the 9.5 update altered the browser in respect to what the last browser update was. (According to UpdateCDN, the last time the browser was updated was 7.1).
So you likely have a 7.1 browser on a 4.x system and the Gateway exploit isn't configured for that and the payloads aren't working like they should.
The safest bet on fixing this is to use a game that updates the system to 7.1 or above. (Game packaged updates do NOT come with the browser, so whatever browser version you have now you are stuck with!)
Pokemon Alpha Sapphire/Omega Ruby come with the 7.2 update. I don't know about 9.5, but 9.4 and below didn't have a browser update since 7.1. So any update between 7.1 and 9.2 will be your best bet on fixing the console so that Gateway works on it again. What version does your browser report as (found in Web Browser's settings menu). I don't know off hand, what version browser that 4.x had. But I'm sure it's not in the 1.7 range. If you have a 1.7+ Web Browser, you probably have the latest one that got introduced in 7.1.
I don't have my 3DS back from being NAND modded yet, so I can't really check what version browser that 4.x normally has.