Yes, mine collects water tho I've not seen as much as you. Most was about 2" with the battery in the case. I drilled 4 1/4" or 3/16" (don't remember which) holes in the batt box to let it drain. Holes in the top, no holes in the bottom and water collects. Who'd think that would happen!
I seem to recall reading another post where the holes were recommended (not my original idea).
2013 F-350 CC SB 2WD 6.7PS
2013 Eagle Premier 351 RLTS
-SOLD- 2012 X23B
-SOLD- 2003 Ford Expedition 5.4, Bilstein shocks