Well, a lot of what you state is really the most important thing, ie if it sounds right, it is right.  Theory helps, but the music was there before the theory.  It helps to think of 3 basic families of chords...then the world is yours. Majors, minors, and 7ths (dominant).  That's it...really.  There are lots of altered tunings, and it sounds like you have found the ones you like..and that's very cool, and probably the best way.  In terms of the finger positions...yes, you can get "bad habits".  If you do things with certain positions (the "correct" ones...) even if the position feels awkward at first, and not comfortable for the hand, it can pay off HUGE dividends later, when the hand starts feeling more comfortable, and with the new position, you are now accessing notes, and chord voicings that would have been difficult if you used the "comfortable" hand position instead. 

If you have the notion, check out Pierre Bensusan's guitar book, simply titled " Livre du Guitare"..ie Guitar Book..it is available at most music stores.  He gives certain hand exercises/warmups, that if done regularly and the way he shows you, will improve your right hand techniques especially, for enormous benefit.  There are also anecdotes, and even cookbook recipes (FOOD,not guitar!), artwork, poems...wonderful!  There is tab with note transcriptions of many of his major pieces. They take a long time to work..but he gives you the whole deal. If fingerstyle interests you...this is THE book.

Gene