There was quite a discussion and in the end, I contacted three manufacturers of focusing aids. The two who answered said not to bother with paper under them as it makes no difference.
Ralph Lambrecht also stated this as did Gene Nocon in his book, Darkroom Printing.
There is a fairly wide depth of focus at the paper stage - much more than the depth of field at the negative. In order to make a difference in the focus position equal to the thickness of paper, the negative to lens distance would have to change a tiny amount. A much smaller amount than you could hope to achieve using the enlarger's focusing control and probably no more than the thickness of the emulsion.
Another interesting test is one carried out by Barry Thornton in his book, Edge of Darkness. He set up his easel on a piece of 1/2" thick board, focused and made a print. He then made two more prints - one without the board and one with a second board. So 1/2" below and above the focused position.
He claimed that he could see no difference in sharpness - and he was obsessed with sharpness!
The conclusion was to use paper if you want to or don't if you don't want to as it makes no difference.