I understand you OP. If you build quality links, it should appear on WMT. However, you can build strong tier 2 links to those links so they can get indexed.
To crown it all, I've discovered that G not showing your links on console does not mean they don't see it.
Personally, I built some links (PBNs and web 2.0s to some pages and google did not show them in dashboard till today but had rankings.