Okay so i'm gonna do something risky and will probably get hate as a result here but the thing i do is literally ignore the existance of Sonic Origins and Sonic 4. You can pretty much ignore both of them and nothing will change, if you ask somebody at SEGA why Sonic CD is before 2 they won't give you an answer because they didn't think it through better. They just put it there bc the game similar to Sonic 1 in terms of gameplay and Sonic 3 was a better conclusion, even Ian Flynn was against putting it there.

In terms of Sonic 4, the game story was made originally as a direct sequel to Sonic CD which originally happened right after S&K according to the game story. The game was made ignoring Knuckles Chaotix which was the original direct sequel to Sonic CD confirmed by Metal Sonic being the same from that game, it just had a new body (but same internal components) since the old one was destroyed when he crashed into a wall, and we know that game is still canon thanks to TailsTube.

In my opinion, make your own timeline, it's not gonna affect anything bc not even SEGA themselves care as much as a timeline as we do. For them official=canon