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joined:Jan 12, 2004
If I had to guess (and I by NO MEANS know what I'm talking about), I'd say the answer to your question is "no". If the SE can't see meta tags on site A or page A (and I was told it can't), then I don't see how it can see links on the site A or page A webpage.
However if you are speaking about exactly as you worded it..."inbound links pointing to site A", meaning you have sites that link to Site A, I do think in that case SE's would see it as pointing to Site B since they would be following the links, and after following the link they would then get the "point" to Site B.