question about fully racked in focuser height

I just purchased a JMI 2" RCF. I noticed that when I rack the focuser all the way in, the bottom of the eyepiece tube of the focuser will project about 1/4" or so into my OTA. I'm using .5" plywood for my OTA. So, when I plug the value of the "fully racked in focuser height" into Newt, should I:

(1) use the height of the racked in tube when the tube crosses the outside plane of my OTA

(2) use the height of the racked in tube when the tube crosses the inside plane of my OTA

-or-

(3) simply the fully racked in height even though the tube dips into the OTA?

thx in advance,
jeff

you should use 3

However if I were in your situation I'd probably mount the focuser out 1/4", either by adding 1/4" of wood to the outside of the focuser board or using other spacers. This assumes that in doing so you don't have any vinetting problems or have to bump up to the next larger size of secondary.