It's not really a matter of DLL format or conversion, in both cases the module is run the same way from Wine perspective.
The difference is that when using yabridge, yabridge redirects the X11 window creation and takes the role of the window manager for Wine windows, embedding them inside its own windows that are in turn managed by the host WM. When running the modules directly, the host window manager does everything.
The problems probably come from yabridge behavior as a proxy window manager, how it manage Wine windows positions and and how it translates coordinates back and forth. This is what was improved in the yabridge wine10 branch, but it's still not completely right apparently.