Different ARO with or without -justDetermineActiveRegions for HaplotypeCaller

I noticed that for one BAM, when calling HaplotypeCaller (I am using version 3.5), with or without the -justDetermineActiveRegions, the ARO results are different at several intervals.

For example, one is (without -justDetermineActiveRegions vs with it):

413386,413388c413386,413388
< chr7  100550695   100550914   size=219    1.00000
< chr7  100550914   100550915   end-marker  0.00000
< chr7  100550914   100551155   size=241    1.00000
---
> chr7  100550695   100550944   size=249    1.00000
> chr7  100550944   100550945   end-marker  0.00000
> chr7  100550944   100551155   size=211    1.00000

This is quite not as expected. justDetermineActiveRegions make the map() return directly without doing any job. This should not affect the active regions if my understanding is correct. But the test shows it does. I may understand something wrongly here.

Could you please give some comments on why the behavior is like this?