"The target can only count the benefits of cover they are in or touching if it lies between them and the Hive Guard."
Actually I think it all comes down to a very small semantic point.
The sentence could be read as:
Only count the benefits of
cover IF X
or as
Only count the benefits of
type of cover Y IF X
It is obviously not written very well but... I think the second is the correct interpretation. Think:
"The target can only count the benefits of (cover they are in or touching) if it lies between them and the Hive Guard."
No effect on the benefits of cover they are not in or touching.
This may not have been GWs intent. Intent is hard to judge but I think this is a rather silly rule if the RAW is what was intended.
However if the alternative was the case the rule would have to read:
"The target can only count the benefits of cover if they are in or touching if it and it lies between them and the Hive Guard."
At least that is how I read it. Again I think that makes it a silly rule, because an intervening unit would grant cover (for example) and I think the intent was to NOT allow that type of cover save. I firmly believe in never attempting to play some bullshit rules as intended because you just never know.