You would have to very carefully explain, in detail, why you can no longer proceed with your processing if you are unable to save your specific files in FITS format. You would also need to specify, in detail, exactly which images you need to be able to save in FITS format, and when in your processing methodology you need to be able to save these in FITS format.
That way, we might be able to help you understand 'why' the use of FITS is just no longer required, and - perhaps more importantly - why the contiinued use of the FITS format is just simply no longer tenable.
The XISF format was not created 'just because PixInsight wanted to use a propietary format', it was created out of absolute necessity. Without the use of the XISF format, and constrained by the now archaic FITS format, many of the new processes in PixInsight would simply not be possible - period.
An analogy here might be, "Do you want to save these files of yours in JPG format?". Almost certainly not! Why? Because you would not accept the loss of information that would occur if 'forced' to use such a format - despite it being perfectly 'portable'. Well, you will soon see that, as PixInsight continues to develop, the FITS format will become les and less usable. As Juan states elsewhere on this thread, the FITS format will become 'deprecated' in PixInsight (remembering that 'deprecated' does not mean 'dropeed' or 'no longer supported' - instead its meaning becomes closer to 'no longer needed') and users just won't think about FITS once they have loaded their data.
Personally, I have not saved a single FITS image since the initial release of XISF.
However, it is only certain key stages of certain key processes that mandate the use of the XISF format. The generation of FITS files at these interim stages would serve no real purpose whatsoever - after all, as already explained, PixInsight would not be able to proceed without the critical extra data stored in the XISF headers, and any third-party programs (that cannot read XISF data ***) would have absolutely no need to be able to read those interim XISF files in the first place.
*** This lack of third-party support is not a problem that PixInsight has created. If third-party software developers choose to fail to implement a royalty-free, open-source, fully-documented, well-established image format such as XISF, then that is their problem. This was always going to be the case, and is why the full XISF implementation and documentation, as well as all source code, was released free-of-charge, long before PixInsight reached this current stage in development, where the use of XISF has now had to become mandatory. These third-party vendors were free to join in on the development discussions, and their input would have served to improve XISF as we now know it. However, when third-party developers have an extremely 'lethargic' attitude to developing their product to meet the growing demands of their existing customers, or if they charge scandalous amounts of money for their customers to enjoy the privilege of having bugs removed from the existing code release, then it has to be the customer that makes the necessary decisions as to how best to invest their money
But, that is a personal (non-affiliated) rant about 'external software' - if this is not the problem that you are facing then, as described above, tell us in plenty of detail about the issues that you are having right now, and we can try and help you.