Everyone naturally wakes up a few times early in the morning but many people aren't aware of those instances (or just forget about them); so waking up a few times really shouldn't have an effect on your sleep hygiene. However, you might only want to use an alarm temporarily to train yourself to wake up because you will often wake up when your body isn't really ready for it (think of it as a sudden change from lower frequency brainwaves to alertness rather than the gradual increase that is normal).

I almost always wake up around 3 or 4am to get up an go to the bathroom - the helps a lot with dreaming (think of the wild and wbtb techniques). I also feel much better when this happens than those rare instances when I don't wake up until a few hours later. So I would recommend drinking water before bed or something like that so you wake up naturally.

When you wake up in the early morning and get out of bed for a bit, you bring more awareness into your next segment of sleep. Also, your brain is expecting to get back into REM sleep around those times, and you may enter that stage sooner depending on how long you stay awake. As long as you are getting enough sleep overall you shouldn't have to worry about losing REM sleep, as it is typically a lack of deep (delta wave) sleep than can cause some problems.