I'm only using the custom lists now for playing tables, but the All Tables list is handy to hide tables from these lists by changing the Rating in PinballX.
After adding [rating>0] to the Xpath queries in the first post (e.g. "/menu/game[type='SS'][rating>0]") i can then go through the All Tables list in PinballX and set any games i want hidden to a rating of 0. As the batch file runs on PinballX startup the next time i start PinballX any tables set to rating =0 will be hidden from the lists. Effectively on my setup this has the effect of disabling the table, but without having to go into Game Manager and remember which table(s) to disable. And if i ever want to try the table again it's still there in All Tables, so i can 're-enable' it during the next PinballX startup just by changing the rating.
It's a pretty handy alternative to actually disabling the tables
EDIT - And if you're using ALT CODE type characters in database xml then you may also want to include the encoding in the xmlstarlet cmd. E.g. the "E Windows-1252" here;
xml sel -E Windows-1252 -t -c "/menu/game[type!='EM'][rating>0]" %SOURCEXML1% >> %OUTPUTXML1%