I seriously undercharged when I started out meaning I had to work as many hours as possible to make ends meet. When I got confident enough to raise my rate, I was able to scale back my hours and work 3 days on freelance projects and 2 days on bootstrapping. The problem I found was transitioning away from the freelance projects (my bread and butter) and dedicating more time to my app which was putting more of a demand on my time as it grew.
In my extensive experience, it can work, but only if you are very disciplined about both the bootstrapping and the freelancing. Decide in advance how long you'll do both, what type of projects you'll take, and the terms you'll freelance under.