Most kitchen fitters will just work out the error as you have and then move the jig off square by the same amount.
Trend do a scribing tool specially designed for this purpose whereby you cut the 1st joint and then place it where it will be going (but on top of 38mm spacers) with it overlapping your other worktop which you have yet to router. You then scribe a line on the worktop and place the jig along the line. It is made to compensate for the collet and
12.7mm router bit. The tool is great, but for a one off job you will get just as good a job by taking care using the method you have currently thought of.
Make sure you also get colour matched jointing compound from the worktop supplier (if they dont have any then pop along to your nearest howdens an get one roughly the right colour) as this makes getting an invisible joint much easier and also seals the joint for dampness.
Good luck Calum Sabey NewArk Traditional Kitchens 01556 690544