What you're attempting is a mid-panel joinery, covered in the user manual:





To do the double twin tenons, you mill one row of the mortises, then flip the end-grain piece (the one where mortises are milled in the endgrain) over to the other side on the mating piece (face grain), and mill the second row.

As long as you're using the baseplate of the machine to reference against the mating pieces, the mortises on the horizontal & vertical pieces will align. Do you have any 2x4 scraps that you can follow the procedure laid out in the manual and make a sample joint?

Remember that the horizontal pieces should be mortised using the baseplate (not the fence) for registration as shown in the above top photo.

for the second set you could use a spacer, lets say about 5/8" thick.
Use the spacer under the base plate to allow the second set of slots.

This approach is even simpler than flipping the horizontal pieces for the second set of mortises.

Any photos to share?

Here is the link on festool using spacers , once I got response from Dirk D , I did some search, found this video.
Took the inspiration and did  twin Dominos using this.



Hope this will give you idea.