Cross-pollination is exceptionally unlikely. It could be a mutant OR it could reflect one of the parent lines if the Jalapeno was a hybrid.

I have a mutant plant from one of 24 seeds started from little asian peppers, it was an indoor plant in my office under a grow light so zero chance of cross pollination. All the other plants were true to type but this one has about 20x larger peppers, the size of mymindex finger on average, and is much milder in heat with excellent flavor. I have saved the plant so that I can work on cloning it since I like it so much.

I don't know for sure where yours came from obviously, but mutations happen more often than accidental cross-pollination when peppers are more than 10-20 feet apart or so... From a neightbor's yard it would be pretty unlikely. Telhat doesn't mean it didn't happen, just that it is very unlikely. Technically speaking you have to be outside of pollinator territorial range to completely eliminate the chance, which is why you tend to hear things like 100 yards, but from a practical perspective being 20 feet away from a different variety brings the chances down very low, like less than 3% I believe.

If you like the flavor I'd consider overwintering the plant and working on cloning it, there is never a guarantee that it will be "true to type" because however unlikely it still could be a hybrid plant, and it sucks to lose a great plant. Sometimes individual plants from isolated open-pollinated species are mutants with desirable traits, like mine seems to be, and there is no guarantee that the seeds I have saved from it will be true to type either, especially since it was closely clustered with two other varieties within 3 feet of it. Still makes for seeds worth planting, but there is no guarantee I will get something similar to the original plant.

Peppers are perennial when weather permits so they absolutely can be dug up, pruned, and kept alive inside over the winter.

Tomatoes are even less likely to be cross-polinated, even by direct neighboring plants, because of the flower structure (no direct pistil access as the tip is shorter than the anthers), so you really don't need to do any intentional diatancing for saving home seeds. The very paranoid could use insect netting around a flower cluster that will be tomatoes for seed-saving, which is pretty cheap and reasonable.