looking at these two CLs:
  https://chrome-internal-review.googlesource.com/460012
  https://chromium-review.googlesource.com/676750

they have a CQ-DEPEND on each other (which is OK).  but when trying to run remote tryjobs, the Bootstrap stage failed.

when given a public manifest config (like chromiumos-sdk), we see:
Preconditions for the stage successfully met. Beginning to execute stage...
11:22:11: INFO: RunCommand: git clone https://chromium.googlesource.com/chromiumos/chromite /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI/chromite --reference /b/c/cbuild/repository/chromite/.git in /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI/chromite
11:22:35: INFO: RunCommand: chromite/bin/cbuildbot --reexec-api-version in /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI
11:22:36: INFO: RunCommand: git clone https://chromium.googlesource.com/chromiumos/manifest /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI/manfest-checkout in /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI/manfest-checkout
11:22:36: INFO: RunCommand: git fetch -f https://chromium-review.googlesource.com/chromiumos/manifest refs/changes/50/676750/2 in /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI/manfest-checkout
11:22:36: INFO: Attempting to create transaction for rahulchaudhry:676750:4eb19b72
11:22:40: INFO: Transaction for rahulchaudhry:676750:4eb19b72 is rahulchaudhry:*460012:*b22f8b18, rahulchaudhry:676750:4eb19b72.
11:22:40: INFO: RunCommand: git fetch -f https://chrome-internal-review.googlesource.com/chromeos/manifest-internal refs/changes/12/460012/1 in /tmp/cbuildbot-tmp4biyGh/tmpKuFFgI/manfest-checkout
11:22:42: INFO: Attempting to cherry-pick change rahulchaudhry:*460012:*b22f8b18:"manifest-internal: sync binutils sources to tip of master branch on aosp."
Trying simple merge.
Simple merge failed, trying Automatic merge.
ERROR: external_full.xml: Not handling case 784937b1f9405f1cba2e3713608676fe1b1e6411 ->  -> 0213a2247d95b60721915f4cf26445631b2de533
fatal: merge program failed
error: could not apply b22f8b1... manifest-internal: sync binutils sources to tip of master branch on aosp.
hint: after resolving the conflicts, mark the corrected paths
hint: with 'git add <paths>' or 'git rm <paths>'
hint: and commit the result with 'git commit'
11:22:42: INFO: Rewinding transaction: failed changes: rahulchaudhry:*460012:*b22f8b18:"manifest-internal: sync binutils sources to tip of master branch on aosp.", rahulchaudhry:676750:4eb19b72 .

when given an internal manifest config (like caroline-release), we see:
Preconditions for the stage successfully met. Beginning to execute stage...
11:24:42: INFO: RunCommand: git clone https://chromium.googlesource.com/chromiumos/chromite /tmp/cbuildbot-tmpHzweUP/tmpMNgulj/chromite --reference /b/c/cbuild/repository/chromite/.git in /tmp/cbuildbot-tmpHzweUP/tmpMNgulj/chromite
11:25:12: INFO: RunCommand: chromite/bin/cbuildbot --reexec-api-version in /tmp/cbuildbot-tmpHzweUP/tmpMNgulj
11:25:12: INFO: RunCommand: git clone https://chrome-internal-review.googlesource.com/chromeos/manifest-internal /tmp/cbuildbot-tmpHzweUP/tmpMNgulj/manfest-checkout in /tmp/cbuildbot-tmpHzweUP/tmpMNgulj/manfest-checkout
11:25:13: INFO: RunCommand: git fetch -f https://chrome-internal-review.googlesource.com/chromeos/manifest-internal refs/changes/12/460012/1 in /tmp/cbuildbot-tmpHzweUP/tmpMNgulj/manfest-checkout
11:25:14: INFO: Attempting to create transaction for rahulchaudhry:*460012:*b22f8b18
11:25:14: INFO: Transaction for rahulchaudhry:*460012:*b22f8b18 is rahulchaudhry:676750:4eb19b72, rahulchaudhry:*460012:*b22f8b18.
11:25:14: INFO: RunCommand: git fetch -f https://chromium-review.googlesource.com/chromiumos/manifest refs/changes/50/676750/2 in /tmp/cbuildbot-tmpHzweUP/tmpMNgulj/manfest-checkout
11:25:15: INFO: Attempting to cherry-pick change rahulchaudhry:676750:4eb19b72:"manifest: sync binutils sources to tip of master branch on aosp."
Trying simple merge.
Simple merge failed, trying Automatic merge.
Auto-merging full.xml
ERROR: content conflict in full.xml
fatal: merge program failed
error: could not apply 4eb19b7... manifest: sync binutils sources to tip of master branch on aosp.
hint: after resolving the conflicts, mark the corrected paths
hint: with 'git add <paths>' or 'git rm <paths>'
hint: and commit the result with 'git commit'
11:25:15: INFO: Rewinding transaction: failed changes: rahulchaudhry:676750:4eb19b72:"manifest: sync binutils sources to tip of master branch on aosp.", rahulchaudhry:*460012:*b22f8b18 .


in both cases we attempted to apply public & private manifest CLs to whatever manifest repo we happened to check out.  the chromiumos-sdk run failed because the private manifest CL doesn't apply at all the public manifest repo, and the caroline-release failed because we applied (successfully) the private manifest CL, but then tried to apply the public manifest CL on top of that which failed horribly.

for the Bootstrap phase, i think we need to be smarter about applying & skipping the relevant CLs.  it might mean that people get a false sense of success if they run an internal-only manifest change against a public bot (or vice versa).  i guess we could issue a buildbot warning and make the stage go orange ?