Do you guys take this into account (from the JL box building page):

The effective length of the port is found by adding an end correction factor. An end correction factor is necesary because more often than not, one wall of the port is also one wall of the enclosure and this wall extends beyond the end of the port thus effectively adding length to the port (remember, the driver can't "see" the length of the port, it can only go by what it "feels" is going on).

Calculating end factor may sound like it would be more trouble than it's worth, but it's actually quite simple. To calculate end correction factor, simply add one-half of h to the physical length you calculated above (L1 + L2).

I take this as meaning I subtract half of the port width from the length.

For example, my calculations calls for a 16.5 x 6.15 x 26.25" long port in order to tune to 33Hz. Does the physical port in the box then become 26.25 - 3.07= 23.18 inches long?

yes