You can still use an Arduino sketch for lower power - it supports chips other than AVR, and even those have pretty good (not the best, compared to ulta low power MCUs) sleep functions. Its the actual arduino boards that drive up the quiescent power - USB-UART bridge, regulators, power supply switching etc..
Using just the bare MCU - programmed with an Arduino compatible bootloader - and a header for a USB-UART cable means you just treat it as an Arduino. - just with the external USB/UART.
The downsides to using the Arduino core is that you're limited in MCU frequency choice, and it'll use up timer0 and I believe the UART periodically fires an interrupt to check for incoming data.
I'm pretty sure you can disable/override that so you can send the MCU to sleep without it immediately waking up to do background tasks.
It's not quite the same as bare metal, but its a nice comprimise between the convenience and familiarity of Arduino, and the flexibility of bare metal.