I am not sure about the F100 but on the D700 it says that you have to set the aperture ring to the largest value. The tab is just to make sure that you don't change the ring by accident. I think that if you don't set the lens to the largest value you will not be able to use P and S mode and you cannot change the aperture using the camera controls. But it should work with A and M mode, but please check the manual for details (I am just guessing here).
I would recommend to set the lens as pointed out in the manual and use the camera controls. This way it is much easier to set half or third f-stop values in case you need it and you don't need to change anything if you want to use S or P mode.
Personally I use M mode every time I have determined the correct exposure (by test shots, camera metering or external metering) and I want to make sure the exposure does not change depending on the subject that I shoot. Example: you want to take pictures of people outside and some of them are dressed in white and some in black (or the background is sometimes very dark and sometimes very bright). You do the correct metering for the skin and you don't want the camera to adjust this correct exposure for the color of the dresses or the background.
In my film days when I shot b&w or color negatives I simply used A mode 99% of the time and it did work very nice (but you need to know when to compensate the camera metering e.g. in snow scenes). When using slides I sometimes used an external meter as slide film is unforgiving and in that cases I used M mode (my camera did not have P or S modes).
Hope that helps