This is more about how various categories of funds are labeled than how things are implemented internally. If you burn M BTS at time t, and then print/inflate by M+N BTS at time t+1, the number of BTS in circulation at any point in time is exactly the same as if you put M BTS into a system account at time t, withdrawing it at time t+1, and printing N new BTS at time t+1.
I agree that correct, transparent accounting of network funds at the macro level should be an important objective [1]. As a community member, I've made numerous forum posts on this topic.
I'm still learning the code. I'm thinking that before I attempt something like this, I should write numerous tests to ensure I understand exactly how the code operates (and to be sure that the code does, in fact, operate in a reasonable manner, even in unusual corner cases).
[1]
https://bitsharestalk.org/index.php?topic=9612