I'm using a RPI 1 but it seems several RPI models have this problem. I'm have tried 8.90.007 and 8.2.5. I'm fairly hopeful that this problem has been fixed in latest libcec 4.0.3. Since the change log states:
Quote* send an active source message when a routing change has been received with
libCEC's address as new route and no active source message has been sent
yet. issue #309 #205 #233
Issue 309 is Kodi Wake up from tv doesn't work
The libcec used in 8.90.007 is 4.0.2 and 4.0.1 for 8.2.5. If this updated libcec 4.0.3 could be included in the next iteration of your amazing creation, it would be much appreciated. The wife is less then pleased with me each time I have to manually activate CEC for her, so you would really be helping me out. Thank you.