Designing vented enclosure

No, the hole through the baffle would be part of the port.  There can be a lot of variations in the box design that the program wouldn't be able to know..such as thickness of the face baffle or possibly part of the port tube extending out of the box.  Just make the physical port the length as indicated and allow space at both ends to complete the acoustical port length (see Help section).

A good vent diameter will allow you to input the maximum power the amplifier will provide to the drivers in that enclosure and be able to maintain a quiet port.  Too small for the power, air will make a huffing sound in the port.  Larger than necessary, the result may be an unreasonably long port length.  Select the input tab and type in the power in watts to be applied.   Use the SPL chart (rear-something, I can't think of it right now) to see the result of the port noise.  See the Help section for details on this, too.  If you can keep it under 110 feet/second at max amplitude it will be good for car audio.  Home audio would want half that, but you are always dealing with compromises within the confines of an automobile.  Larger port openings necessitate longer port lengths, and sometimes you just don't have the room for it.  So reach the best compromise that you can in this area.

SPL for rap...where you decide the tuning freq to be will not only involve the type of music but the combination of driver / enclosure.  Use the program to model a Cheby (sp, you'll see what I mean) enclosure.  You'll note the response will peak, not a flat-as-possible response.  Peaking in the 40 to 45 Hz range would be ideal for your posted intention, but work with what you have in any case to see how it looks. 

Take your time with this program and refer to the Help section as often as necessary.  You'll find answers to all your questions about it that you posted, and more.  Good luck.

Yeah, I referenced a couple of songs that I checked out with a freq program.  Just to show that some of the lowest bass notes we hear in popular songs are still above the 40 Hz line.  For SQ, I would tune as low as possible, but I'm not relying on SPL from the port with those, either.  But for SPL, I want to tune just below the majority of bass hits, and with most popular music that Fb would be in the mid 40s.

Here's a pic taken directly from the WinISD Pro help file.  This is from the newest alpha version that's been out for a couple of years:

The amount of space at the ends of the actual, or physical, port is basically an unknown factor.  You just need to use some rules of thumb:  on the inside, leave at least the diameter of the port.  On the outside, leave at least that amount of room as well.  Those airspaces act as functioning parts of the overall port length but are not figured in port length measurements.  The program looks at the end of your port by what you input into the "End correction" box under the "vents" tab.  The 0.732 that you see in the window is the default and works with most port installations, and should work with yours.

For SPL, decide whether you want to use meters or feet with the program.  Use the options from the drop down menu and click to choose.  Also click to choose whether you want to see "peak" or "rms" port velocity.  I personally like to use feet, and also would rather see the rms velocity rather than the peak.  It seems to me that rms, which is going to be a much more manageable port size, is more in line with other software programs (see link below). 

110 ft/sec is 1/10 the speed of sound in average temperature at sea level.  Unless you're in the mountains, that can be a general guide to use.  The rule is different depending on what kind of system you're dealing with and who you talk to.  Car audio, as I mentioned above, is rife with compromises by necessity.  Space and weight are issues.  Car and road noise is a factor as well.  Because of these very real wrenches, my opinion of acceptable port noise is different with car audio than it is with high fidelity home audio.  Where I agree with 5% of speed of sound for the home, I am willing to accept 10% for the car.  So, 110 ft/sec or below at RMS power is fine with me for the car, as I very likely wouldn't know the difference with all the associated noises the car environment has.

It sounds like you're doing well with your enclosure.  Consider installing a subsonic filter on that if your amp doesn't have one.  You can set it below the Fb but not too far down.  For 43 Hz tuning, you can put a 35 Hz ss filter on it and be fine.  Use your test tones for testing during setup.

https://www.the12volt.com/installbay/forum_posts.asp?tid=50823&KW=winisd for more of my input on using this program.