Hmm, i cannot confirm, if differences in PCB are really that minimal in this particular case, but question seems interesting in general. For cases of custom PCBs to have only little differences and need slight adaptation, imho it's really worth to release V2 of block with those updates, instead of not releasing any but initial for reference PCB, or instead keeping producing both V1 & V2.
Probably though extra care should be taken for alignment of inlets of V1 vs V2 to be same, for SLI/CF water bridges to be usable between diff. versions of blocks. And as some of such custom PCBs are of higher height, then maybe design inlets spaced higher above side of even reference PCB card V1 blocks since the beginning in future.