I'm sure, they do count as the absolute values (which can be considered as the negative % when below the certain number for your level).
And I guess the number that you see when you support your friend is this "extended average".
Here is my example:
I have a 109.2% (52.3) main eleven (and I can get this number by averaging their levels)
+ 4 subs:
12. Mbappe is 104% (51),
13. Lunyaev is 1% (16) ~ -35% in fact,
14. Shimansky is 1% (14) ~ -44% in fact,
15. Zero is 1% (9) ~ -62% in fact.
When my friend (same level as I) comes to support me he sees: 44.1 (which is equivalent to 75% for level 6).
This is much lower than if they were counted as 1%, lower than best 14 average and even little lower than if I take the average of all 15 players (including -62%(9) one which is out of the best 14 will give 77.6% (44.6)), which confuses me a little bit