We already have a contextual popup menu if the mouse hovers above an object. E.g. if the mouse is above a block, the left button will setup a start or end point for a route that you want to create (or cancel). The right button activates a popup menu, where you can, if a train is in that block, select to display details about the train or the block, and if there is no train on it, just the block details and you can toggle the maintenance flag. There are similar popup menus for switches and signals. Now, if the mouse is over empty space, then there is no popup menu right now - so we could add a popup as you said covering the special cmd options that you mention, plus the re-center.
The manual override allows you to lift a block restriction on a one-directional block to temporarily allow travel in the opposite direction (TDP btw never had that functionality).
The pass-red-signal function can indeed be added as an additional item to the popup for the signal (signaled permission) or as a possible response to the engineer when in communication with him (oral permission).
