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Your system has no way to signal to applications that its recycle bin does not exist/is non-functional. Every other operating system has a well-defined API for recycle bins that the user can configure however they like, including disabling that functionality, centrally. In typical Linux fashion, all there is is a half digested spec for a few folder locations, that people like you feel free to ignore and then blame other people for when your expectations break.
It is not calibre's job to somehow read your mind and figure out what you want. You want to break the commonly used paradigm of the recycle bin, then it is up to you to break it in a way that does not break software that depends on it. For instance, I too dont use a desktop environment, but I long ago setup a script to deal with the recycle bin in a fashion I like. I certainly did not whine that it is every application maintainers job to provide a setting to cater for my special snowflake setup.
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