Excuse my bad English. I use that system a lot. For smooth work:
1.- Process each Raw, correct color, etc. and save as TIFF.
2.- Finally, open a New focus stack or a New stack with all the TIFFs.
The Mac will work much faster. I make 40 or 50 TIFF batteries and it takes you a few minutes (little time).
I have not used Focus Merge for a while, and I have just tried it in version 1.8.3. It does not have an align box, because it does the alignment automatically. I suspect that if your images are poorly aligned, then ther automatic alignment will not work. The only thing is to do it the hard way.
If you have an aligned stack of layers (either from New Stack or simply by manual alignment, then follow the instructions given by @walt.farrell here. This allows you to export your aligned files in a convenient folder from which you can then apply File > New Focus Merge.
Note that I had previously been referring to File > New Focus Stack, when I should have been calling it File > New Focus Merge.
John
Kosakdeschamps got a reaction from walt.farrell in Stacking images - Affinity seems to "lock up"?