When activated TNT falls into an endportal, the TNT will be in the ground in the end.

Intended, entities can enter just as nether portals.

That's not what I mean. If the TNT by Endportal to end passes, it is in the ground.

The issue is that it is in the obsidian, not on top of it.

Confirmed in 13w04a.

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Fixed in 14w28a/b? I don't know.

This seems to have been FIXED some time during or before 1.8.1-pre2.
http://gfycat.com/FittingSecondhandAntbear