I know almost nothing about this. I believe it's "normal" for Nasm to strip the "." from ".text" or other section names, and just pass "text" on to the linker. Is this causing a problem?
I have no idea why your alignment is being changed. Possibly the only alignment allowed by that output format? Normally, "gcc" would imply Linux, or other *nix-ish OS - "-f elf" - but gcc could also be used with djgpp - "-f coff" - or with mingw/cygwin - "-f win32". I doubt if it will help *me* to know which, but it might help others help you...
My only suggestion is "RTFM" - both the Nasm manual, and that of whichever gcc you're using. There may be a clue in there somewhere. If you figure anything out, please post!!!
Best,
Frank