My "middle aged" A54 has the front cover that you guys reference. 

I drilled a few additional holes in the bottom of the rest of the cover. The original Amel setup has one small hole and when I opened up all of the covers to service the outhaul motor/gearbox, there was some water pooling.

I do believe that water can readily enter from the top near the shaft. Specifically if it runs down the outhaul rope track. When we give the boat a good freshwater wash, water definitely streams out of the holes I drilled.
--
Scott 
2007 A54 #69
SV Tengah
http://www.svtengah.com