Every time i have to select "Unix", encoding is correctly preselected as "utf-8" according to my "Settings->IDE settings->Default file encoding".

Tools->Settings->IDE settings->Default File Format

Regarding encoding, there are the following places to check and they are used in this particular order:
-Workspace->Properties->Default encoding (it works for the file's directory and all directories above up to the project root)
-Project properties->[Properties] button (right to the Root directory) ->Default Encoding
-Tools->Settings->IDE settings->Default file encoding

sorry, i meant not encoding (works correct), but file format. Just try to create new php file and save it. "My Tools->Settings->IDE settings->Default File Format" (Unix) is NOT preselected in file save dialog.

This depends on the actual file format in the phped\templates directory. You may want to open template for php (and any other) file type and save them with Unix line endings.