but [Pomodoro's] rigidity doesn't lend itself well to a lot of tasks that I deal with - reading papers and writing code, mainly. In both cases, it takes a lot of work to wrap my head around things, and I lose that if I take a break at the wrong time.

I definitely have this problem too, now that I write a lot more code than I used to back in Aug 2013. You may be interested in my proposed solution, the Pomodoro for programmers.