One solution to the Rebels ISD debate that might work - simply say that all references to "ISD-I" in Rebels tie-in media should read ISD-II.
That just leaves the tractor beam array to explain - as a refit or later model variation, between Rebels and TESB. It's a lot easier to imagine one ship component changing, than a whole bunch of components. Something like:
"a new model of targeting array was developed by KDY, and proved to be so much better than the standard array, that all ISD-Is and ISD-IIs were refitted with updated arrays"
This also handily explains why the ISD-Is in TESB, while present (seen flanking the Executor as it arrives at Hoth), do have slightly different arrays.