My thought on the subject is not so contrasted.
Without even talking about the dangerous side of wiring an internal transformer, there is also that without a faraday cage it adds noise to those analog circuits... and additionally also heat.
But if it's properly made, OK it can be interesting. In my opinion the main advantage with an external one is to keep the case littler. So as here the case is bigger than it could for the angle desktop style to be achieve, it could contain an internal one.
HappyMum wrote:ElSchtroumpf asked me (by PM) Nava box dimensions:
The dimensions are exactly the same as Yocto, so wooden sides Yocto match on Nava box

I would like to point out that if the PCBs are of the same size as the Yocto one the case is for sure not the same size as the ElSchtroumpf Yocto case nor the Kacper one, it would then be in fact a bit littler. Here the 90° angle is made between the bottom and the rear, like ElSchtroumpf did at the first time for the prototype. But then he changed it for the 90° angle to be between the rear and the front, which added a bit of room in the case to be able to put an internal transformer more easily (and also gives a nicer profil and more accessible rear for the plugs).
For sure the wooden sides Yocto which would matches that you are talking about are not the ones I made.
Here is a
PDF with the ElSchtroumpf case's profil (blue line for the lower part and black for the upper one). It can be printed in 100% and give the real size. Could you clarify the size aspect a bit HappyMum ?