No, what I was saying is that if you wanted to ensure that the siphon standpipe started more reliably, you would drill the hole for the bulkhead for the open-channel standpipe 1/4" higher than the hole for the bulkhead for the siphon standpipe. If you read enough of BA's thread you will see this suggested several times. What I was saying is that you cannot do this, since it's already drilled.
As far as drilling a hole in the siphon standpipe, I think you're referring to drilling one just above the water line in the sump to aid in purging the siphon standpipe during startup.
The reason that your settings probably didn't make a lot of difference is because of the nature of BA's design. You are supposed to have 2 down-turned elbows, and when the siphon kicks in full, it will suck the water level of the box down to below the level of the lowest point of the open-channel (horizontal, inside the bulkhead) because the opening of the elbow is below that level. As long as the water stays far enough above the open end of the siphon elbow, it won't suck air and lose the siphon, and as long as the water doesn't go too high in the box, the open-channel standpipe will only get a little water flowing in it. The point is to tune it so that water just flow down the open-channel.
I think that by cutting the end off the downturned elbow of the siphon standpipe, you may have lost part of the functionality. The siphon now cannot lower the water level in the overflow box as far as it could before, therefore your "tuning range" is decreased. It depends on how much you cut off the siphon elbow. Of course, if you didn't turn the open channel elbow all the way down, maybe just pointed it sideways, you would still have a little tuning range, but it still will never act as a true backup siphon.