The one thing that does not handle well is secret/concealed doors-passageways.
I've taken to putting a letter "S" on the Hidden layer and including a macro on it, a la your Timer token. Selecting the "S" and clicking the "Search" macro runs a Search check on all PCs on the map sending the output to "self". (I plan to add DisableDevice and OpenLock macros as well.) I should probably save a list of those who succeed on the check so that I can refer to it later (scribble-scribble on an electronic post-it note). I also have a single macro that move the "S" token to the Object layer so that the players can see it.
It should be a simple matter to tell the "S" token that there are other tokens that should be moved to various layers on success, allowing the OpenLock check to make a passageway visible. Probably properties like "Token", "Object", and "Background" where each is a list of token names that are moved to the respective layer upon success. Maybe have a similar list of tokens that should be moved to the Hidden layer as well? This will need tweaking, since I wouldn't want it to happen unless I specifically authorize it.