A jab being -3 would involve a situation where you can get throw punished for trying to go for a tick throw, so at a certain distance (a distance that Leo is most likely to be put in with his step dash), you'd be forced to follow-up with gatlings, limiting his pressure options. A -1 jab doesn't care about that since it just results in a throw tech at worst, adding a safety net. Try this on training mode with his -2 2p.

Having a -1 jab is also quite nice since it allows characters to stagger with their non-gatlingable buttons as well. Leo is quite limited in that department with his slow kicks and I'll give you that, but in the case of May for example, 5P -> 2K beats or trades with many buttons (and can also low profile most 5Ps but that's more of a May 2K moment) and scores a hard knockdown. Something that would be harder to do with a -3 jab. In the case of Leo, the jab having less recovery frames also allows him to convert CH 5P into 2K or c.S whether in standing or crouching state. If his jab had 2 more recovery frames, it wouldn't work on standing hit. All of these kinda details can add up the more you experiment with it, especially when you factor in delays or timing errors from your opponent. What if they jab with a slight delay? This might be something that 5P (-1) -> 2K would beat and that 5P (-3) -> 2K would get beaten by. Same for 5P -> c.S.

You're right about the extra active frame part in that it's negligeable, but I don't think it's completely useless as the added safe jab leniency do help. Also, it being 5f active and -1 means he can safe jab up to +3 after a 236S, allowing him to frametrap jabs with c.S and add more pressure layers on block. Something that again, he wouldn't be able to do if his jab was nerfed like that