A beta of 3.0 has been posted (download here) that supports both remotely editing INSTEON links and having Indigo send INSTEON group/scene commands.
Remotely Creating and Editing INSTEON links
See the Indigo online help for more details.
Creating and Sending INSTEON scene/group commands
See the Indigo online help for more details.
Controlling KeypadLinc button LEDs via scenes
From within any Action panel (inside a Trigger Action, Time/Date Action, Action Group, Control Page click action), select a Group/Scene number you want to correspond to a KeypadLinc LED and enter an optional group/scene name in the edit field. Press the Add/Edit Devices... button, then (in the new dialog that opens) select your KeypadLinc in the responder popup control. Next, select the popup control to specify which LED you want to control (ex: controls 4th button LED). In addition to using this scene to control the KeypadLinc LED, you will probably also want to go ahead and control the device(s) associated with that KeypadLinc button (LampLinc, SwitchLinc, etc.) so that the device turns on/off in unison with the KeypadLinc LED. You can add those responders to the scene as well via the New Link to Responder button.
When you are done press the Sync Now button, wait for Indigo to update all the links, then close out of the edit dialog. You can then test your scene via the Test Send On and Send Off buttons in the Action panel.
Unfortunately, you have to create a new Group/Scene for every KeypadLinc button LED you want to control. This is a limitation to how INSTEON groups work and how they are, in this case, being used to control the KeypadLinc.