add option to check for missing columns in compareFlatTrees

During my previous changes I had to realize that our tests don't flag columns disappearing, which is not ideal. This now adds the option to check for that as well. I added that as an option so as not to change existing behavior.

I enabled that for the CP algorithm checks, but had to disable some columns that the sequence configuration didn't have at all or had different results. I'm not sure if it is worth fixing this (given that the sequence configuration is on its way out), but if so this should be part of a future change (given that it currently also doesn't get checked).