Yes, it is a bit confusing. However, I wouldn't let the presence of variable crossover settings on one receiver be a major influence in choosing one model over another.
The problem, easily overcome, is that when you use the line-level "subwoofer out" connection on most receivers, the receiver inserts a low-pass filter (crossover) fixed at around 80 Hz (THX models specify this frequency). (Non-THX receivers may use a higher or lower fixed frequency.)
Most powered subwoofers also have an internal crossover variable between about 40 Hz and 150 Hz. And most subs don't let you bypass this crossover (some do). So, the problem arises because you have two low-pass filters "cascaded" when you only need one. This isn't a big liability if you set the sub's variable crossover to its highest frequency (approximately) and let the receiver's fixed crossover roll off the highs and pass the lows.
Some receivers, like the one you're considering, let you choose the frequency of the low-pass filter. 80 Hz is a good place to start. If you set it much higher--over 100 Hz, for example--you risk running bass frequencies into your sub that are directional, and you don't want that under any circumstances. The sub should NOT call attention to itself.
It also depends on the individual low frequency response of your main left and right speakers. You want to avoid a "hole" in the transition from the subwoofer to your mains and center channel. With some experimentation, by tweaking the sub's internal crossover and--if you get a receiver with selectable low-pass frequencies--the receiver's as well, you can arrange a smooth sonic transition between the sub and the rest of the speakers in your system. So a receiver's adjustable low-pass filter does give you some added versatility. However, you will always have to fiddle with room placement of the subwoofer. Standing waves (bass reinforcements and cancellations) exist in all rooms and finding an ideal location is a matter of trading off compromises. Avoid square rooms at all costs, because standing waves are at their worst in such rooms.
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