It really isn't bad where you play at all. Playing closer to the neck gives a deeper, rounder sound (more like an upright bass), but the strings have a lot lower tension there so you have to be weary of fret-buzzing, playing over the pick-ups usually gives a pretty crisp sound (depending on the bass of course), and playing near the bridge gives a brighter and punchier sound, and the string tension is heavier so it may be easier to play quicker back there without fret-buzzing. A lot of players may go from one location to another in the middle of songs.
The only thing I'd be concerned about is getting comfortable with your thumb on your pick-up. It may limit your movements and/or slow you down. I personally like the floating thumb technique, where I lean my thumb against the lower strings to mute them as I play, and when I'm on my lowest string (an E because I play a 4 string), I leave my thumb floating there as if it was leaning against a string above. I just slide my hand and thumb up and down as I transition from string to string.
EDIT: And I just re-read your post and it seems like you may contorting your hand to play in between the neck and the pick-up while the thumb's on the pick-up. This could cause wrist problems. The first concern in right hand technique is to keep your wrist straight, no sharp angles. You should practically let you hand dangle in front of the strings, your hands should be very relaxed, and not forced into any position of any sort