Not 100% sure since it isn't clear in the rules, but RAW it doesn't say that you're "shooting" anything when using Markerlights, it just says that you're "picking an enemy".
Nothing is fired, you don't roll to hit or wound and you forego your own shooting to use it.
Remember that you do need LOS to the model you're "marking" though, so you would need to bear that in mind if you're in cover that'd block your LOS.
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