Well, before we get too far off into the weeds (flashing) I will first have to agree with Lim Wee Haut - it is pretty unlikely that the bootloader has any effect on charging whatsoever. Tablets that are pure stock can pull 1.8-2A from the Asus OEM charger, so it's not obvious that software is ever the problem.
For instance, when the tablet is booted into the regular OS, it is impossible for the bootloader to be active. It's not like a PC BIOS (where software interrupt calls from the OS can be vectored through the BIOS). At most, the bootloader could set some hardware registers (e.g. in the SMB USB/charger chip) prior to loading the Linux kernel, but once the kernel is active, it is free to reprogram the hardware through it's device driver(s).
And what about when the tablet is completely off? This situation is less obvious to me - after all, when you plug the N7 onto the charger, a "charging animation" is displayed, and *something* is painting the screen... but I don't really know if that activity is being run by bootloader code or something in the tegra3 "miniloader".(The Tegra3 has a small ROM area in it for storing a tiny executable that can be programmed by the system designer and then protected by use of private keys)
In any event, the problem could be the charger, the battery, the cable, or any number of other things. Note that it is possible to observe the charging current using the "Current Widget" app plus a kernel that has the bq2745 current monitor patch in it, but you need to crank down the max clock and screen brightness - what you observe via that app is literally the current flowing ONLY in to the battery, not the total current provided by the charger. That means - because you can only get the tablet down to about 300 mA of consumption with the screen on - that the most charging current you will observe that way is about 1400-1500 mA on a charger that can put out 1.8A @ 5V.
OK, back to the flashing thing: I skimmed through two of the threads related to the "bricksafe flatline" hack, and I got the impression that once you have used that hack, there is no going back to fastboot for flashing bootloaders any longer - you are stuck using nvflash/wheelie thereafter. Is that incorrect? Or was it just that using fastboot with that patched bootloader (4.13-hacked?) causes flashing problems? It would be consistent with what you are reporting.
Sorry for the apparent randomness of this reply, just throwing out some ideas.
"I'm gonna start coding placebo apps. That way I will be sure that the complaints are real and the praises hollow."