Hi Orestis,
Wonderful report that was a pleasure to read. Excellent job in observing these two -- I looked at both last night too.
The enhancement you saw near the core of NGC 253 is almost certainly not an HII region. This eg is an exceptionally dusty one and in very large aperetures under true dark skys it looks finely mottled over quite a bit of the surface. There are a number of low surface-brightness spots (that are star-clouds) around the core that are contrasted with darker spots. Undoubtedly, this is what you have seen. The brightest one is not far outside the core to the southwest.
You are right -- it's not quite edge on.
Though it is somewhat surprising, in infra-red images it looks like a tipped over NGC 1365 -- NGC 253 is in fact a barred spiral when you look at it at this wavelength:
http://www.nasa.gov/mission_pages/WI...gc253anim.html
compare to NGC 1365 (superb image here by Mike Sidonio) and the similarity is striking.
http://www.pbase.com/strongmanmike20...85050/original.
Your best chances of seeing an HII region in another galaxy (outside the local group) is actually in NGC 55 that you also observed.
Okay, the core is off-set to the NW and you saw that, but apart from the core could you see any other spots along the major axis of the galaxy? There are two others not hard to see in 10" class 'scopes. Both are HII regions. NGC 55 is basically an LMC analogue (a barred irregular/small spiral) about 5 million ly distant seen edge on and is pretty lumpy -- like the LMC.
Well done!
Best,
Les D