I get what you're saying and it's possible to implement all that, but the current workflow is what it is for a reason. Applying modifiers to collections would result in too many UX surprises and pretty bad footguns.

What you want would be less of an issue in a tool that allowed for a more procedural approach where the assembly of complex objects is part of a modifiable construction history that is separate from the final scene graph. In such a context, merging objects is technically destructive, but repeatable. I've written such a modeler once.