Regarding the "omit a field" question, I'm surprised that there's not an easy way to do this, but I can't think of anything beyond what you have tried so far. I think if you write a custom routine that simply returns null, that should do the job, but there ought to be an easier way. I think it would be nice to have a "dropFieldIfFieldEmpty" modifier similar to "deleteRecordIfFieldEmpty." Hopefully Bob will step in and provide an answer if there's something I simply don't know about!
As for setting upperCaseSubfields in a config file, I think it was Bob's intent to move away from config files in favor of command line parameters, so the current config file handling is kind of a thin layer designed for backward compatibility, but it may not be forward looking. I agree with you that config files can have some advantages, so I wouldn't mind if this were improved and made more flexible... though it's also been on my radar to consider reworking VuFind's scripting to rely less on configuration files, in case the built-in SolrMarc support goes away in the future. (Though it hasn't gone any further than being generally on my radar, given many other priorities that have taken more of my attention 😊).
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