GCLK->CLKCTRL.reg = GCLK_CLKCTRL_ID_USB | GCLK_CLKCTRL_GEN_GCLK4;GCLK->CLKCTRL.reg = GCLK_CLKCTRL_ID_EVSYS_0 | GCLK_CLKCTRL_GEN_GCLK4;.....
Why does this technique require the removal of the bootloader? Doesn't the bootloader run only once when the board is initially powered up, and from then on it's never executed again unless you press reset or the PC attempts to initiate a serial connection? (I assume the code that performs that check is part of your sketch, not the bootloader itself.)
Then, as trampas mentioned, point all unused peripherals to dead clocks like so:
Surely re-pointing all the generic clocks isn't necessary, as all clock sources: XOSC, XOSC32K, OSC32K, OSCULP32K, OSC8M and DFLL48M, that don't have their RUNSTDBY bit set are automatically switched off in standby mode anyway.
Plus, it is recommended on the "Atmel AT06549: Ultra Low Power Techniques" application note chapter 7 (:
But that's only relevant if the generic clock is being driven by a clock source that's active during standby.