Probably found my error: I was calling "gcc" instead of "ld" for linking step but did not add "-Wl," for the linker directives.
Now when using ld (i.e. in fact arm-eabi-ld) the alignment (in the elf file Program Header) is the same for Linux as for Cygwin.
Maybe this answer can help somebody else facing the same problem I had.
Cheers
Philipp
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