Thank you for responses.
@firstdefence Yes, merge visible seems to be working exactly how it should, yet when I have e.g. larger project file with 30+ layers-groups, function Merge Selected feature is essential, so I don't have to constantly hide rest of the layers when I want to merge just 2 of them.
@GarryP If feels like there is some automatization missing in this, because what is it for user if he has to do this all the time. I often import images from google, edit them and import them to my project file where I usually want to merge them with others. Is it expected to machinate with Transform Panel everytime I do this? What's also weird for me is that something like Force Pixel Alignment or Move By Whole Pixels have zero effect on this.
Edit: Few typos