Wow, I feel bad that you have to go through all that extra work when reloading!I have used three powders so far: WST, WSH, and RS Comp. WST and RS Comp both leak a little. The WSH doesn't leak much. I am just living with it. I blow the press clean with dust-off periodically. Eventually the powder mucks up the stage 1 collet so that needs the partial disassembly and cleaning mentioned in the manual. Checking the counter bore depth sounds like a good idea. I don't use the primer dropper so I use the its mounting location to attach a small piece of wood to minimize the powder that drops down onto Stage 1. Sometimes I put a small paper cup on that piece of wood to catch the powder leaking out the end of the bar.
If you're using a MEC progressive loader you should consider having it gone over by MEC.
It should not leak to the extent that modifications are necessary to load ball powder.
The only time I've removed a collet in the past 35 years is to replace when broken. Never to clean. This is never necessary for a properly running loader.
Also, if you upgrade to the large capacity primer tray you will eliminate all the downside to using the older trays. When installed and adjusted correctly, it's a joy to use!
Maybe your loader needs a little TLC to get it back to it's original running condition.