They actually both contain the same innards, the difference is in the packaging. The 4600 series stands alone while the 8900 is designed to be a drop in replacement for the existing converter section of your power center.
One thing to consider is the distance between the power center and the batteries. Often the power center is located close to the AC power inlet and there's a fairly long wire run up to the batteries. Long wires (more than a few feet) choke off the bulk charging current. If you're going to boondock and use a generator to recharge the batteries, consider getting the stand-alone model and put it close to the batteries for maximum bulk charging current which will shorten the time you need to run the generator.
Don't mount the converter in the same compartment due to the battery gasses, but in an adjacent area. Just plug the converter into an AC socket and wire it directly to the batteries The existing wires will carry the power back to the DC fuse board in the power center, just like they do when you're boondocking.