Adv TDMS is designed for performance. On Windows OS, in order to use 'disable system buffering' for writing performance, it require sector-align data for very write to disk. So, Adv TDMS will create a 4 KB header and fill the gap with zeros.
The best use case for ADV TDMS should be that set the header information at the beginning and then keep logging the same-layout raw data. If you need to call the 'set channel information' repeatedly for your scenarios, then STD TDMS is more suitable.