No, the blame is entirely on WinBoard.Ferdy wrote:What Lima did something wrong here?
When starting the second engine for analysis, WinBoard fails to apply a feature timeout, and proceeds before it has had the chance to receive the engine's feature commands. So it treats Lima as a v1 engine, where it assumes the engine plays the currently selected variant. But it doesn't pay attention to the size overrides there (which arguably is another bug, in the support of v1 engines), so it assumes the engine plays plain 'shogi'.
In non-size-overriden variants you would not notice this bug, except that you would fail to get this popup when the second engine does not support the variant. (Well, you would notice it if other essential features were ignored, such as setboard=1.)
This only hurts when the second engine has not been used yet. If you have used TwoMachines mode before, or opened the Engine #2 Settings dialog, WinBoard would already know all the engine's features, and everything would work well.