@emanuensis - You're right I did swap facto & jure - my excuse is that it was early morning and I was low on caffeine
What aggravated me that it was obvious that you had not bothered to browse the database schema. Had you done so then it should have been immediately apparent that there were no Large Binary Objects in it - I'm not even certain SQLite even supports them, in the sense that Oracle and DB2 do.
As to the other items, de
jure standards do exist, your use of word 'violate' implied that Calibre does not conform to those standards - which is palpably untrue. To write that it violates them might be regarded as unlawful in some jurisdictions under the laws of libel.
As to the 'gist' of your complaint - the Calibre source code is available for download, and you can make whatever changes you want so that it conform to your requirements, for your personal use.
I bet most users of Calibre (here are the usage statistics ==>>
http://status.calibre-ebook.com/) don't give a rat's left elbow about folder names being mixed case or having spaces in them - because they never look them, because under normal circumstances there is no need to do so.
Now imagine someone decides to stop using calibre. They will find their ebooks stored in a folders whose names are comprehensible, maybe not to programmers, but a mere mortal should have no difficulty finding their books.
BR