I see these differences in lenti-Cas9-2A (compared to lenti-Cas9):
- Absence of a bleomycin resistance. That just affects cloning
- Changing from a CMV- to a RSV promoter for lentiviral mRNA production: That promoter is used for the host cells that produce your lentiviruses. They might react differently to different promotoers. So in the end, your viral titers might differ, when switching these plasmids.
- Changing from a bGH- to a SV40 polyA signal polyA signal. That might affect (production and) half-life of lentiviral mRNA both in your lentivirus producing-host cell culture and your mouse small intestinal organoids after transfection. You might want to start your research here: Humes et al. 2020
Together, I think both plasmids should work just fine. I'd say that the observed differences affect mostly how well your host cell culture performs in producing lentivirus. And these difference might differ a lot between cell types. But like I said, it's just the lentivirus production. If you got enough virus to apply to your mouse organoids for gene editing, it doesn't matter.