Hi,
I suppose you have find the answers already, it has been a while when you post the topic. Anyway, here are my thoughts:
1. As far as i know the TWR-SER module is actually the part of the kit. But, that was few years ago i ordered some S12G tower kit.
I suppose the new kits include the proto board, but you've got some older stock.
Not sure what was the price of the kit you paid, but twr-ser is much more expensive than twr-proto.
And yes, if you want twr-proto, order it separately.
2. The MCU module TWR-S12G240 has a 6-pin header J23, close to the D1 and SW6. The J23 header is used to select the power supply source. If the jumper is in 1-2 position, the power from elevator is sourced to the MCU module. Therefore, in case you use MCU module as standalone, the jumper in J23 should be set accordingly (VB is the USB power supply)

3. I am not aware of video-trainings for S12G. The most relevant document is the S12G reference manual. Besides that, the AN4455 is just right thing for you. It comes with the PDF and detailed description. More examples you can find here on community, just search 'S12G examples'.
4. Either.
Regards,
iggi