When you change a single colour in Bootstrap, it changes a series of classes - affecting text, backgrounds, buttons, hover effects, gradients etc… Searching for ‘primary’ finds 59 occurrences in a Bootstrap .css file I just tried. If you were to change all the colours with all their related classes, in a custom css file for example, it would be a huge task.
Once you’ve set things up (which as you suggest, is not a trivial matter), you could choose your colours and the relevant changes (possibly hundreds of them) would be applied in a second or two.
There are other changes you can make like switching on gradients. There’s a single SASS rule to set this. Again, it would be a difficult and fiddly task to create all the relevant custom styles.
Having said that, if you only need a few changes, custom css styles may be the best solution.