Bootloader difference between Atmel328p(through hole) and Atmel328p au(smd)
The bootloader doesn't care about how many pins the device has. All it cares about is the UART pins, and they are the same.

Internally the two chips are the same, it's just the packaging that is different. They take the same silicon chip and mount it on a different lead frame and encapsulate it in epoxy. Which is why the only pin differences are a couple of extra power and ground pins, and two dedicated ADC pins that they don't connect in the DIP package.  Even the pins are in the same order around the chip if you examine the pinouts in the datasheet.

Whether you use the DIP (Uno) or the SMD (Nano) bootloader it makes no difference (the two bootloaders are the same anyway). There can be no "perform better" anyway, since that isn't a valid concept. Either it is compatible, in which case it will work, or it's not, in which case it won't.

The only real thing of concern is to ensure that your fuses are set correctly for your chosen clock source, and that the bootloader you install is compiled to run at the speed of your chosen clock source. That has nothing at all to do with which chip it is you are using, but how you have designed your circuit.