Q1:
Your interpretation of the "Rare rules" of 9th is flawed, I think. They do not say
"Any time cover is referenced to interpret it as Light Cover", they say exactly this:
Sometimes a rule will tell you that a model or unit gains
the benefit of cover, even while they are not entirely on or
ina terrain feature. If a model or unit is under the effects
of such a rule, and that rule does not specify what the
benefits of cover are, when resolving an attack that model
is assumed to be entirely on or within a terrain feature
with the Light Cover terrain trait
It deals exclusively with models that gain Cover while not actually being in Cover. There is, however, a section that follows with the title "IGNORING THE BENEFITS OF COVER" that has this excerpt that I think strengthens the case for
SS:
Ifa rule says that the target unit ‘does not receive the
benefit of cover, without specifying what benefits are
ignored, then, when resolving an attack with that rule,
models in the target unit ignore all benefits received from
all terrain traits, including those that improve its saving
throws, impose penalties on hit rolls and so on (e.g. Light
Cover, Heavy Cover).
Shadow Strike doesn't deal with the removal of any benefits, but it simply states "+1 against units in Cover", which ought to mean any Cover. I would also argue that there's a difference between being "In Cover" and "Receiving the benefits of Cover", that's what the entire Q1 kinda revolves around.
A unit can be standing in Heavy Cover, which doesn't matter for shooting, but still
SS would receive +1 to shooting attacks in my opinion simply because the unit is in Cover (whether it's functional or not).
Q2.
"Stalker" is triggered when standing wholly on top of an obstacle though, right? Wholly on or in a terrain feature is what matters, and an obstacle is a terrain feature. Standing on it ought to work, bizarre though it may seem?