Hi....with my limited knowledge.......short answer....no......the work offset is the centre of the spindle as 0,0 on whatever you set it to....the corner of the vice jaw for X and Y etc.
Putting another different diam tool in the spindle means the spindle centre line still stays the same at 0, 0 but you would have the diam of the tool applied in the program as a different tool offset because it's a different diam to the first tool, so the tool path is set over the respective amount to allow for the half diam of the next cutter.
In the program you would call up tool #1 or #2 and the program would apply the necessary tool offset for each of those tools that you have previously set in the tool register for each tool.
If you just changed the tool holders over without designating the tool number in the program Masch3 will think you are still using tool #1 because it's a stupid program and can't think like you would.....unless you tell it otherwise
Ian.