As a practical matter, since you're the editor of the puzzles you can "get away with" whatever you wish. There's nobody else to reject your puzzles for not meeting the rules, other than the risk of people not buying or using your game.
I suspect most crossword solvers, and in particular those who do so as a sporadic recreation, don't particularly care about the "rules" of symmetry or word length, but rather are concerned with how fun (and how challenging) the puzzle is to solve.
Of the two, I'd probably be more likely to get rid of symmetry before using two-letter words. Making interesting clues for two-letter combinations is tough, especially without resorting to abbreviations of some sort. I'd very definitely avoid one-letter "words" (or their equivalent, non-crossed squares); I'd also attempt to avoid splitting the grid such that two sections are connected by only one word if at all possible.