From the wiki:

Short on the MPU causing F115 to blow
There is one more way for the 12VDC power to be lost and for F115 to blow. A shorted IC on the MPU that uses 12VDC can cause F115 to blow. To help isolate the problem to the MPU, replace F115, disconnect power going to the MPU at J210, and turn power to the game on. If the fuse does not blow, the problem is almost definitely on the MPU board. Any of the LM339s (theoretically) or the ULN2803 (definitely) can fail and short 12V to ground, causing F115 to blow.

I think you missed his point. You should not measure current ever by bypassing the fuse as you no longer have overcurrent protection and a short can easily blow more components. It's the same problem whether you measure across an installed blown fuse or if you pull one end of a good fuse out of the holder.