Bob, you actually did the stereo upgrade I considered doing with my 2014 JKU Rubicon. I've got the Alpine "premium" sound system too and it's FAR from premium, in my opinion. The sound quality was pretty awful for what it claimed to be!
Over on another Jeep forum, a few guys have been doing a lot of work on trying to improve this system without spending a lot -- trying to find the "ideal" upgrade steps.
I think they've generally agreed that the Infinity 6032si is the way to go in the sound bar. (Take some poly-fill; that polyester pillow stuffing you can get at any craft store, and put a wad of it behind each of those sound bar speakers too. It will add a bit of clarity to the sound, as it prevents the plastic of the sound bar from resonating at certain frequencies.)
For the front speakers? I'm not so sure I would have gone with the 6032si up there, for the exact reason you've stated. You wind up doubling up on your tweeters in front when you do that. I see no harm in just disconnecting the factory ones at the top of the dash -- but then you have the disadvantage of your tweeters firing down near your knees, which isn't ideal placement for them.
I opted to keep my factory front speakers in place on my Jeep right now, and I did a modification to the factory tweeters where you solder a 4.7uf capacitor onto each of them. If you have no experience with electronics or soldering, you probably have no interest in attempting this one .... but it really was a worthwhile mod. Only cost about $5 and it adjusts the frequency range that gets to the factory tweeters. (The way they came from Jeep on the 2014's, it almost appears somebody screwed up and used the wrong value of capacitor. It winds up filtering so much of the frequency range out that the tweeters seem to be barely working. Before I did this mod, I couldn't tell any sound was coming from the factory tweeters unless I held my ear right up to one of them. Now, it's obvious they're working while sitting at a normal distance from them in the driver's seat.)
What I haven't done, but thought might be the optimal solution, is buying a pair of the Infinity 6032cs speakers for the front. These are true component speakers, with seperate tweeters and mid-range drivers, plus an electronic crossover you're supposed to wire up in tandem with them.
My thought was, you could at least try using just the midrange drivers out of one of these sets, putting those in the front dash, and leaving the factory tweeters in place.