I just wonder if Mach recognizes the difference between a limit switch and a home switch

I mean lets say on the input pins screen if I put a pin number for the X+ and X- or if I put a pin number for the X+ and Home, does Mach knows the difference?

Not really sure what you are asking but heres how Mach sees things. If you have a pin and port set for a home switch and it is the same as you have for a limit switch then when any of these switches are hit Mach will E-Stop. However when you tell Mach to home it will treat the switch as a home and will ignore it as a limit until homing has completed.
Hood

The reason I’m asking is that I had to put my Y and A limit switches on the same terminal in my BOB (to free one terminal for the zero touch plate for the Z axis). Later I thought perhaps that was not a good idea because I may not be able to home the Y & A axis.

If both Y & A axis are on the same terminal in BOB, would I be able to home Y & A ?

I have the X & Z on separate terminals on BOB because to change the wiring for them its a major job. However if I have to do it in order to be able to home properly I will do it.

But then again if X & Z are on the same terminal, would I be able to home these two axes?

If Y and A are two sides of a gantry, then you have to have separate home switches on each side.  X, Y and Z or X, A and Z can be on the same terminal, but A or X respectively need to be on a separate terminal in order to square the gantry when homing.  If you don't want to square the gantry, then just use a single switch on one side of the gantry and tick "Home slave with master" on general config.  You don't really need a limit on both sides of the gantry anyway.  On side should be a limit/home and the other a home on a separate pin.

If Y and A are two sides of a gantry, then you have to have separate home switches on each side.  X, Y and Z or X, A and Z can be on the same terminal, but A or X respectively need to be on a separate terminal in order to square the gantry when homing.  If you don't want to square the gantry, then just use a single switch on one side of the gantry and tick "Home slave with master" on general config.  You don't really need a limit on both sides of the gantry anyway.  On side should be a limit/home and the other a home on a separate pin.

You mean A or Y respectively need to be on a separate terminals ?

Yes I want to square the gantry

To square the gantry, each side needs to be on a separate home switch.  One side can be limit/home and tied in series with the X and Z, but the other side needs to have a home switch on a separate pin.  This assumes that A is slaved to Y.

Got it, no problem and thanks