1 I've never met this usage before, but I'd guess it means that the second figure is an approximate estimate (as if the speaker had scribbled a quick calculation in pencil). When something is 'pencilled in' it is arranged provisionally: 'Let's have lunch next week. I think I can make Wednesday, but I need to check when I get back to the office. Pencil it in, and I'll ring nearer the time to confirm.' But I don't think 'pencilled out' could be related to that.
2 Not a stick sort of stake, but a gambling sort of stake - having some financial involvement in the outcome. If the company does well, the employee benefits (probably through the share price). FYI - someone who has a stake in a company is called a 'stakeholder'.
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