I believe the chance to get seeds back isn't quite 100% even with the crossbreeding soil, but I'm not entirely sure.. It helps to have some in reserve before you start so you can make up the initial lost seed and any potential lack of seeds afterwards.

You can plant a (iirc) mandrake in that final open slot after planting the jute and that'll give you another chance at a jute seed when you harvest it.

If I recall correctly, I just planted Jutes and mandrakes and ended up with like 30+ additional jute seeds by the time I got bored of hoarding Jute. Does take extra time to gather the mandrake seeds though, and I think it has the potential to give you a different seed. But I did this before they changed finished plants to no longer wilt (or at least I didn't know about the change).