Boot mode related query

Hi post following the forum topic: (1) R7FA2L1A92DFM: Programming connector - MD pin and RES pin related query. - Forum - RA MCU - Renesas Engineering Community

I did understand the MD (P201) is a boot mode selector pin that when set to GND and MCU reset results in SCI or USB boot mode selection. Here are my queries (Could not reply back in the same thread).

1. If JTAG/SWD Pins are disabled by the user still, can we enter boot mode to upload binary? 

2. What determines if Boot mode will come up as SCI mode or USB-CDC mode as I want to fix the mode to USB-CDC?

3. Does Renesas has any flashing tool for PC or any python script that helps in uploading the binary to the flash via USB-CDC so that we do not need to develop such a tool as on a high level I understood that programming is not a simple UART we need to make boot loader understandable packets, seems a tedious job?

4. I see that the on board JLink circuit connects MD pin as well may I know what is the reason for it? Does SWD/JTAG has any dependency on that pin?

5. Where is the bootloader code stored in the flash? Is it part of the memory map? Can any way that part of the code be modified by JTAG?