V speeds are only any good if everything is working as planned. As soon as something is "out" they are pretty much useless. Wrong thrust settings, wrong flap settings, wrong data input and taking off from the wrong part of the runway are all commonly seen mistakes that can really spoil your day. Fudging the speeds by calling V1 early doesn't really solve your problem. We had an A330 where the crew entered the ZFW into the EFB and took off with a V1, VR and V2 all about 40 knots too low. They did exactly as your guys did, firewalled the levers as they approached the end of the runway and managed to get airborne and somehow saved the day.
I guess trusting your instincts is as good a protection as anything else when something has gone Pete Tong.