All palettes have only 16 colors though they would have space for 256 ... only 16 are used in TIM, TIM2 and TEMIM. I know it's hard to believe but it's true. The compression used in SCN format is not very effective. They would have done a better job storing 2 pixels in 1 byte instead.
This is the in-game palette of TIM (the first color is transparent):

Here are two examples (formatted and commented in my hex editor):
PART23.BMP which is 16x16 and the SCN section contains 127 bytes of compressed data:

PART28.BMP is only 16x15 in size and the SCN section contains 137 bytes of compressed data:

The compressed stream seems to always end with 0 followed by 64.
I've modify the resource files to see how the sprites change in game but that did not reveal much because a lot changes by modifying a single byte.
Any hints appreciated, I've stared at these numbers for too long now already

movAX13h