While onboard powered subs in a speaker can cause problems in optimal speaker location, their voicing, being that the manufacturer has control of that aspect, trumps the separate sub or subs in some senses. One such instance is the ability to integrate the sub into the overall frequency response pattern, a benefit which answers to some degree the main drawback of adding subs to a system. Cabinet resonance must be dealt with and getting the best ball response and imaging from the same location requires careful placement. In my experience the placement of this type of speaker is even more critical than normal. This was brought to my attention by Jim Smith and I must say he was on the money here.
Nodes are another factor where having the subs in the same location as the mids/tweeters can cause issues. But to be sure dialing in the correct placement of separate subs can be frustrating as well, not to mention speaker cable placement and ability to have the subs in a user friendly location.
All in all, I worked it out to my satisfaction and wouldn't change anything. The balance in the spectrum built in by the manufacturer overcomes the downsides, at least in my experience.