Rough sketch of what I think the implementation will look like:

• There's no storage for Buildable transactions yet, so create HarbormasterBuildableTransaction, a new class in storage/. It can mostly be a copy/paste of HarbormasterBuildPlanTransaction and HarbormasterBuildStepTransaction. That is, this should subclass PhabricatorApplicationTransaction.
• Add a table for it. This can mostly be a copy/paste of the schema changes which add the above tables.
• (You don't need to add a comments table, I don't think making these things commentable is too useful.)
• Create a new Editor -- HarbormaterBuildableEditor -- like HarbormasterBuildStepEditor and HarbormasterBuildPlanEditor. This will subclass PhabricatorApplicationTransactionEditor.
• Create a new TransactionQuery -- HarbormasterBuildableTransactionQuery -- like HarbormasterBuildStepTransactionQuery.
• Add a constant to the new Transaction for TYPE_COMMAND or similar, to record "some user issued a command to this buildable".

Then the view code looks roughly like this:

$xactions = id(new HarbormasterBuildableTransactionQuery())
  ->setViewer($viewer)
  ->withObjectPHIDs(array($buildable->getPHID()))
  ->execute();

$xaction_view = id(new PhabricatorApplicationTransactionView())
  ->setUser($viewer)
  ->setObjectPHID($buildable->getPHID())
  ->setTransactions($xactions);

...and you'll add a piece of code when the restart/stop/etc command issued like this:

$xactions = array();

$type_command = HarbormasterBuildableTransaction::TYPE_COMMAND;

$xactions[] = id(new HarbormasterBuildableTransaction())
  ->setTransactionType($type_command)
  ->setNewValue($the_command);

$editor = id(new HarbormasterBuildableEditor())
  ->setActor($viewer)
  ->setContentSourceFromRequest($request);

$editor->applyTransactions($plan, $xactions);

Finally, implement methods in HarbormasterBuildableTransaction until the transactions render sensibly.