Having been working with old M's and Model F's for the last few weeks, I actually have begun to appreciate the two piece keycaps.
It means that I can cap and test keys before I have to worry about what exact final layout I'm going to implement. I can only assume that was IBMs conclusion as well. Since keyboards report scancodes based on the position of the key and not "what the letter is", it means they could put keep the same-ness of all the different layout models further in the manufacturing process. Also, for the end user, it would have been easier to wash.
And I honestly can't feel the difference between the two.
I do tend to use my old-IBM keystems whenever I can, but I really don't have a good reason to do it... I just do.
On a separate note, I've always wondered why unicomp doesn't sell the tops and stems separately.