Photoshop has trimmed transparent borders for as long as I remember and I have been using Photoshop for 20+ years. The trimming can change alignment when you align layers. To prevent that what I do to keep the transparent borders when I want them kept I put a 1% opacity pixel in the top left corner and bottom right corner of the image so there will not be any transparent borders. There are no pixels pasted in the areas where there is no pixel data empty areas and you not going to see the two 1% opaque pixels in any print or on your display. Why wouldn't Photoshop trim a layers bound to a rectangular area where the layers pixels are. How could empty pixels be copied to the clipboard there is no pixel data. I would also expect if you have Photoshop copy a selection or layer the only thing Photoshop should copy are the pixels selected or partly selected. How do you copy nothing on top of pixels or into other documents in area that may be outside the other document canvas area. You seem to know how Photoshop works you need to use this knowledge and work accordingly.
If everything that could be as option was made an option Photoshop may become even harder to use for you would need to set more and more options and may you may remember how you set a option from time to time. Like the options that Adobe added to Photoshop CS4 the broke old and new actions that add adjustment layers you may forget how you need to set the options before you play the action so adjustment layer may not get added the way you expect them to. Adobe chooses not to fix this problem.