Since Photoshop is by its legacy a print-oriented image editor, the current behaviour makes complete sense: you would get the same result in Illustrator and InDesign when importing those two images with those document settings.
Print-oriented design applications take no heed of the actual pixel resolution, and always scale an imported image based on the relation between inches/cm/etc. and the number of pixels per inch set for that file. (ppi - I wish people would stop abusing dpi for screens - it is pixel per inch, not dots per inch which are used when talking about the actual print on paper). Anyway.)
The ppi is a completely arbitrary number, which can be changed for an image without resampling it, thereby effectively changing the physical size of that image in a document.
As it stand, that is how it works, whether you like it or not - what you suggest is to completely disregard the ppi setting, and just work with the actual pixel resolution on the screen. That would be perhaps more convenient for screen, mobile, and web work, but that is not how Photoshop sees things. I would suggest that you set the same ppi for all your files (without resampling, of course).