Shortening of the analog path will reduce possibility of interference as well as noise from passive components (i.e. E12DIY is fully shielded from EMI where E12 isn't), better layout of the circuitry can improve separation, lesser active components that generates noise, especially in the power section, too will improve SNR. More current can be fed to the amp section because less is needed elsewhere. Even as you have said - by removing bass boost, you can free up a little bit of headroom that would otherwise needed so bass boost won't result in clipping. All the little bits add up.
Yes, that's a blind test. I won't say it is laboratory standard, but it is as close as it can be done in a home, with SPL meter and multimeter to match things up.