This one is more of a opinion really.
I like the idea of having a master dosbox.conf file, and then if you have special settings for a game, only those settings are added to the game specific dosbox.conf file.
Here is how it works, I have the standard dosbox.conf file, but I have a game that requires the machine type to be tandy. Instead of having an entire copy of dosbox.conf for the game, you just have this,
[dosbox]
machine=tandy
When you start DOSBox up, you use
dosbox.exe -conf "dosbox.conf" -conf "game.conf"
DOSBox then merges the two .conf files, with game.conf taking precedence.
The reason I like this, is if you change your mind and want to make all your games use a different scaler, all you have to change is the master dosbox.conf setting, and all your games will now use the new scaler.