Long story short, Intel PT is a byte-code which aims at minimizing the output size. Therefore it uses tricks that make it hard to recreate the code execution path w/o doing so-called 'full decode'. Full decode is slow, therefore honggfuzz is doing partial decode, which is way more precise (lowe number of recovered program blocks) but way faster.
The way to change this is to implement full decoder for Intel PT, which will use the fuzzer binary as an input. Apparently WinAFL started doing that some weeks ago, so mayb the code could be reused.
With BTS what is stored by CPU are all branch/jump src/dst addresses, so it's more precise in this sense.