Jdm is factory built engines with lower miles. If the shop you're dealing with does just import motors or has a lot of experience with the 5vz then I would go ahead with the rebuild but a lot of times jdm motors have less than 100k (we know that's practically brand new for the 5vz) and that's awesome.
The other thing about jdm is that they are imported engines from japan. It's not that they are super or anything but it's a law over there to maintain your vehicle. Every 2 years you have to pass what's called a JCI and it's basically giving a mechanic carte blanche with repairs if your car doesn't pass.