2 year home residency is must n it can't be bypass

I hope I understand your question. It should not matter if you get visa stamped or not. If you are in J1, you are entitled to 2 year residency. But if it is waived, you can get visa stamped and come back easily to US. You will have to goo back to Nepal only when your J1 is expired and your 2 year residency is not waived.
Here is the tricky part with J1 transfer. You can go from one employer to another (no matter what position) but only when your 2 year residency is not waived. Meaning, if your 2 year residency is waived, you cannot come again in J1 even with your same employer after you j1 program ends.
I hope I answered your questions.

@ ma Nepali: If 212 (e) does not apply is tick marked by consular in DS 2019. I am not sure it will apply.
@bbmb: Thanks

Can I take another higher position or should I remain in same position? For example if I am research assistant, can I transfer university and change title to research scientist or research associate with same J1 status?

so you have not applied for waiver thing?