No, it will not be more prone to rear main seal leaks. It will be just fine.
The difference is the way the lifters are held down if you're using a hydraulic roller lifter. In the older blocks, you either have to drill/tap the lifter galley for a lifter spider or use link-bar lifters. The newer roller blocks already have that provision.
Everything else should be interchangeable with the exception of the water pump. The newer blocks had serpentine setups, which requires the water pump to be a reverse rotation pump. If the short block already has a timing chain cover on it, you can look at it and see which water pump it's set up for as this is not block specific....i.e. you can put a serpentine setup on an older block, or run a regular v-belt system.
For a lower rpm street engine, you will not notice any differences between externally/internally balanced assemblies.
With the main girdles, there are some that are larger than others and have a step-out where the
oil pump is. These will cause some interference with front sump pans and sometimes the pans have to be "massaged."