I actually prefer atlas (see: https://github.com/nim-lang/atlas) to nimble now, it clones dependencies to to a local `deps/` folder relative to the project. It also supports adding local folders to the nimble path for management (via `atlas link` - see docs here: https://github.com/nim-lang/atlas/blob/master/doc/atlas.md#l...), i.e. you can clone your dependencies yourself via git submodule or a manual git clone

To solve your woes, fork and patch the code you need to in order to support pragmas for MSVC. And in atlas, use your fork's git path and if you choose to: submit a PR to the project. You can edit the project locally until something works.