In T369548, @Aklapper wrote:

without telling me who created it (usually it does so there might be an upstream bug but no steps to reproduce, maybe the "Duplicate Form" thingy not creating a transaction entry?) with no way to ask what the intention was.

Duplicate Form is some WMF thingie: https://phabricator.wikimedia.org/rPHAB893664bd44b86b36e3775fb0843bd4c2019de1c2.
So this is a downstream bug.

PhabricatorApplicationTransactionEditor::applyTransactions() checks if $is_new = ($object->getID() === null) to set $this->isNewObject; adding $new_config->setID(null); to PhabricatorEditEngineConfigurationSaveController::handleRequest() makes no difference.
Probably ->setTransactionType(PhabricatorCoreCreateTransaction::TRANSACTIONTYPE) would be the right thing to do but we do not have any field object for that, only a full config that we copy.