Season 1 and 2 are both based on the original manga, ending at episode 62. Season 3 is all filler, every last bit. 63 is a bit of a shoutout to Kenshin's past but it's just to tip off that they aren't doing anything else from the manga. There is a noticeable decline in quality until the Shimabara arc, and after that it drops off horribly again. 100% skippable, but potentially entertaining.
After episode 62, you start reading from chapter 152 in order to continue the series with Kenshin's past. This is the written version (mostly) of Trust & Betrayal/Tsuiokuhen. You finish with the rest of the manga's Jinchu arc.
Reflections/Seisouhen is the closest thing you get to an animated version of Jinchu. Unfortunately, this is also of sub-standard quality. This is quite the shame because there's supposed to be even more fights than in the second season.
There's also a "filler" movie, Requiem for the Patriots, and a 2010 "update" for the Kyoto Arc where everything is thrown into a pinball machine. You can watch these, too, I guess.
The only real differences in adapting Tsuiokuhen are...... that the events are slightly shuffled, but this was the correct change to make for pacing.
The manga didn't bother to blur the age difference between Kenshin and Tomoe.
Tomoe cuts the rest of Kenshin's scar while dying in the anime; she does it almost by accident in the manga.
Most importantly, the manga clarifies that it was Kenshin's idea to "pretend" to be married.
In addition, the manga version carries the sort of tense but comical tone of the rest of the series. Tsuiokuhen is dead serious the whole way through, zero laughs expected.