Not necessary, all you need is to able to access to SSH.
If you flash using Prometheus scripts, it should able to handle the rest.

For Mi-Mini, you have an option to flash Breed bootloader following instructions in the 1st post.
With Breed, then you can flash .trx directly.

Not sure I got any good advice for you.
If I recalled correctly for my MI-3, I have similar failure for backup.

Since I didn't change to Breed bootloader, I figure out if I need rescue, I could always restore to Xiaomi firmware using the UBOOT.

I went to update the source, configure the packages/addon and flash the firmware via Prometheus Scripts.

Yes - You can flash without backup the partition. Of coz on your own risk to do so.

As for the configuration, answering direct from my memory here, you should follow the steps:-

Option(0)  to check if the script can ssh to your router
Option (1) to update the script
Option (2) to update the source
Option (3) to build toolchain (this will take ages - many hours)
Then
Option (4) related to firmware.
Once you are in, the sub-menu options available to:-
-configure - simple mode or by editing (notepad styles - disable and enable option with '#')
-select skin
-update source again (no need if you already done so)

Then the same sub-menu would allow you to:-
- build the firmware (this will take ages - many hours)
- and lastly flash the firmware.

Hope this help.

The way I did it.now is build the firmware then I flash via padavan web GUI from the router.

I only use the scripts to build firmware.

Not sure I understand ur question here.

1st time, I would recommend using Prometheus and subsequently okay via padavan.

Why? Because i been told xiaomi firmware and padavan have different partitioning. 1st time to make Prometheus will partition and flash it.

Subsequently you and run using padavan from router web page (firmware upgrade) and check the log to see the flashing. You will able find from the log which partition is flashed.

For those who lazy to build their own firmware.

Links below is only for those already running Padavan and interested to update to latest commits.

USE IT AT YOUR OWN RISKS.

MI-3_3.4.3.9-099_9cdd85a.trx
https://mega.nz/#!txASgabD!ZhbpocG6...n4B6_izbKQZZLPM

MI-MINI_3.4.3.9-099_9cdd85a.trx
https://mega.nz/#!01pmVCQA!tFEooJux...DEO0ckn5QTnlf1k

Cheers.
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Assume you already have your VPN working with direct ip from the wan/router.

Goto WAN -> DDNS to configure get dynamic address, example: yourname.ddns.net

Before this you need to register and create a domain from example of  dyn, no-ip.com, change-ip.

Check your home folders, you should able to find it.