I have never installed or modified a set of DSE connectors. But I would think that if after cutting them down you boxed them back in you should be ok. It will decrease the overall strength of the connectors, but for anything less than a full on race car i THINK would work ok.
They don't come in too far, is there some other thing that will cause a problem if you don't cut them down?
Maybe one of the builders or someone with DSE connector experience will chime in.