General questions for JR Pass

Hello,

We are planning a trip on September and we are wondering if the JR Pass (7 days) worth it for our planned route which is the below:
Tokyo-Kyoto
Kyoto-Osaka
Osaka-Tokyo

Based on the calculator it seems that the cost is almost the same if we order the pass or not. Is this calculation includes bullet trains?

Also, what else is included in this pass? Are regional or subway trains in Tokyo included?

I understand that we cannot make a seat reservation online but we should do it each time at the station?

Thanks in advance!