The check if a marker for a portal was already created only looks into the current chunk of the player. If a nether portal goes over chunk boundaries, one marker gets created in each occupied chunk.

There won't be another 1.12 update, so I'm closing this.

Also, those markers don't work at all in recent version...

This would be nice to fix, but it should be rare.

Actually, it may not be as rare as one could think. Consider the standard 2 wide nether portal (for wider portals it's even worse):

There are 256 = 16x16 blocks in a chunk. And 64=16x4 blocks right next to a chunk border (I'm counting edges corners twice because they have two chunk borders. This means you already have a 1 in 4 chance to place a block right next to a chunk border when you randomly place a block in the world. For each of the border blocks, 1 of 4 directions will place the nether portal across a chunk border. Thus, you have a 1 in 16 chance to hit this issue, when you place a nether portal randomly in the world. That's not what I'd call rare :)

Markers are stored in "marker chunks" that are 8 times bigger than regular chunks.
Btw have you actually encountered this issue, or did you discover it by reading the code?