Two things concerning the creation of new TMs
>After creating and saving a new TM (and starting the project) I get after one or two segments confirmed a prompt to save the new TM. This dialogue not only pops up and disappears under the main window (I need to minimize the main window to access it)
Yep. On my Mac too. Always wanted to report that.
>it also asks whether I want to replace the old file.
Yep. Very counter-intuitive. Looks almost like the Save TM command invokes the Save TM as command. Please change this. Same when merging a folder with TMX files to one TMX or after opening a Studio TMX file with filtering and saving it for the first time. The already existing name isn't used without first asking if this is okay. Of course this is okay.
The pop up hassle happens also on Windows.