The 2007-11 CBA specifically addressed the fact that compensation picks were not to be counted toward the total number of choices (at that point, 15 rather than the current 10) which were protected from free-agent compensation.
Here's the pertinent passage from Article XX, Section B (4) (d):
The Regular Draft Choice of the signing Club described in subparagraph (c) above shall not include any selection in the Rule 4 Draft awarded as compensation for failure to sign a Rule 4 Draft selection from the preceding year and shall be assigned as follows. If the signing Club is among the first half of selecting Clubs, excluding selection(s) awarded as compensation for failing to sign a Rule 4 selection from the preceding year
, then the choice to be assigned for the highest ranking free agent Player signed by such Club shall be its second choice . . .
The boldface there is mine, to emphasize the specific exclusion of compensation picks when determining which other choices weren't subject to free-agent compensation. Compare that to the parallel passage from the 2012-16 CBA, which is Article XX, Section B (4) (c) (i):
A Club that signs one Qualified Free Agent who is subject to compensation shall forfeit its highest available selection in the next Rule 4 Draft. A Club that signs more than one Qualified Free Agent subject to compensation shall forfeit its highest remaining selection in the next Rule 4 Draft for each additional Qualified Free Agent it signs. Notwithstanding the above, a Club shall not be required to forfeit a selection in the top ten of the first round of the Rule 4 Draft, and its highest available selection shall be deemed its first selection following the tenth selection of the first round.
Note that no choices, compensation or otherwise, are excluded from the group of 10 protected from free-agent compensation. That language has been removed. Furthermore, the language is pretty clear: a club's "highest available selection shall be deemed its first selection following the tenth selection of the first round."
Now I won't blame the Mets and GM Sandy Alderson for appealing to MLB that they should hold onto the No. 11 overall pick if they do sign Bourn (which I still think is a longshot). They'd simply be trying to seek a competitive edge. And I'm not surprised that the MLB Player Association would support the club, because a favorable decision would enhance Bourn's value.
But the owners and players agreed to the new CBA, which clearly removed the language that wouldn't have included Pittsburgh's Appel choice in the total number of selections exempt from compensation. The rule was changed for a reason, and to alter it the first time it's inconvenient for a team would be silly.