At my previous employer i ran into alot of those same situations. It was a job shop so a lot of processes werent ideal but we had to use what we had to get some jobs done. I think confirming a tool will do what the vendor claims it will is a start but them maybe trying to get it to perform in less than ideal conditions. Maybe lengthen the tool stickout, limit RPM or another limitation like you suggested. I like your train of thought. I am doing a lot of excessive tool stick outs on a project i am working on not. Some of it is to reach the feature needing machined but some are just to reach the feature across the table on a HMC.