Well...actually, that's not exactly correct, but I can see your line of thinking. Whether it was a column or floor shifted automatic, the neutral safety switch was activated by the the shifter lever - but it is all hooked together. If you were to keep the stock shifter and just remove the linkage, your NSS would still work.
The linkage system was there so that you could not shift the trans out of park unless you put the key in the ignition switch and turned it to the "run" (or start) position. I think it's commonly referred to as "ignition interlock" or similar. It was a safety thing. You needed the key to get the thing out of park, and you needed to be in park before you could remove the key. Kept the curtain climbers from playing in the car and taking it out of park, etc. Interferes with lots of header brands, so many are long gone.
To answer your question - if your car was originally a column shifted automatic, without the linkage installed you will lose the function of the NSS that is on top of the coulumn. Your aftermarket shifter should have come with its own NSS and it's a fairly simple process to wire it in. Look for 12ga purple and purple/white tracer wires to your existing switch and extend them to your new switch which will likely be mounted on the shifter body somewhere.
The column shifted automatics had the switch mounted on the column. The floor shifted automatics had the switch mounted on the shifter base. If you swapped from column shift to factory floor shift and kept the interlock linkage intact, you could retain the column mounted NSS and the linkage would activate it. You might be able to do that with your aftermarket shifter provided you can find a trans lever that will accommodate the interlock linkage, but I think most aftermarket shifters are a universal design that probably won't include the correct lever.
