it is very common for WinISD to suggest a larger enclosure size than reccomended by the manufacturer for a couple reasons.
Most typically sealed enclosures are suggested smaller because the typical person sitting in a car really wants a peaky subwoofer responce. Most music will peak in the higher subwoofer frequencies, rarely diving as deep as a subwoofer will travel. The smaller sealed enclosure will create peaks higher in the frequency range, where more music will be represented. Also, an added benefit of this peak is it puts the enclosure peak closer to resonant frequency of the car. This creates an additional spike, and one LOUD note. Also, it is easier to sell a subwoofer in a smaller box... who wants a 3 foot enclosure in their trunk

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Ported will be reccomended smaller and typically tuned higher for the same reason. Both size and peak I mean. A ported app will be suggested as an SPL enclosure (almost always) because of how the subwoofer will react and output at tuning... also typically very close to resonant frequency (imagine that).
I like to look at WinISD pro for a couple graphs. Don't forget to add your supplied RMS power in the signal page!!! I do suggest you look at impedance. See how the woofer enclosure will affect the power delivery from the amp and set your gains accordingly. Also, look at excursion (bear in mind on ISD it is peak to peak) and see if you stay within the realm of linear travel while designing your enclosure. Also, you will need to watch for woofer unloading and set the subsonic filter accordingly.
http://www.eatel.net/~amptech/elecdisc/caraudio.htm This is by far the biggest source of information I can think of to maybe help explain the hows and whys more than I can. Also,
http://www.diysubwoofers.org/ , is a wealth of info on subwoofer enclosure charachteristics and design.