While the linked video isn’t a speedrun, it may be possible that using Kenya the Spearow instead of Totodile would end up with a faster route. Since Kenya is a physical attacker, it gets much better use of its physical attacking normal and flying type and even gets mud slap for coverage against steel. Additionally, it’s much faster than Feraligatr and even gets boosted EXP. you can see in the video how STAB return was one-shotting nearly everything near the endgame.

And unlike Nidoran in Red, you don’t have to waste time in the grass looking for Spearow since you get this one right outside Goldenrod. The only downside is you can’t give it a single letter name to save time, but the better stats and speed might make it worth it

A French runner named UnderscorePoY made a Spearow+ route for Crystal (not Kenya) and got a 3:40 with it :
It enters Goldenrod at level 17 (so 7 levels above Kenya), and loses 14 minutes to the current Crystal WR between Whitney and Red.
Considering the 7-level deficit, even accounting for the possible optimisations to the route (and for the small differences between Crystal and Gold/Silver), there is absolutely no way you can go faster with Kenya than with the current route...

If Kenya was Level 20 (like it is in HG/SS) there'd maybe be a chance (especially in Gold / Silver because no Raikou) but yeah sadly 7 levels less is too low.

Mud-Slap would also be good against Rock types like Onix too, as well as help in Morty's gym (probably)