Electronic – freechargecontroller.org. The blocking diode of the MOSFETS

I am looking at a schematic for a solar charge controller:
http://freechargecontroller.org/images/a/ab/Charge_controller_4_04b.pdf

My question is about the MOSFETS M1 and M2. The data sheet for the MOSFETS I am attaching:
http://www.jameco.com/Jameco/Products/ProdDS/669943IR.pdf

I think I understand that there is a blocking diode inside each MOSFET that allows for the flow of electrons from the source to the drain
but not in the reverse direction and that diode is called a body diode. It is shown in the data sheet for the MOSFET. I am looking at the way the
source pin of M2 is connected and it appears to me that what is connected to the source pin of M2 is a conduit that runs between that positive
terminal of the battery and the source pin of M2. There is an inductor coil on that conduit. Hopefully I will be corrected if this is not exactly the case.
It appears that J2-2 also ties into the same conduit and there is a blocking diode D3 in place there.

If the source pin of M2 then has a positive charge and there is a blocking diode inside M2 then wouldn't that blocking diode in M2 prevent the flow of electrons from
traveling from the drain of M2 onto the VS line when M1 and M2 are activated?

Also I think I understand that diode D2 and capacitor C2 are providing a bootstrap voltage but I'm not really sure yet how that bootstrap voltage is generated exactly or
what it is exactly used for. Could someone explain?

Thank You