someone else ran into this problem - did around on the community for that post if you can.
i don't know if he found a solution. if you are good w/ the blcli you could write a nsh job that looks for the last run of the PAJ, find the created remediation job, then the deploy job and waits for that to finish before exiting. that would hold up the batch job exectuion.
We have had a somewhat different problem that we have not resolved. For us, the deploy job that is generated by the Analysis job is never actually executed (we have execute job now set). We were told it was a 'known issue' with patch analysis jobs in 8.0 and that they would only automatically execute the generated deploy job if the server was a default target of the analysis job (e.g. could be run with 'execute' instead of 'execute against'). I'm surprised you're not having the same problem given that you are on the same version/SP as we are.
Looking for the last run of the analysis job runs into the fairly common problem of concurrency issues - if two instances of the analysis job are running at the same time you will pull back the same job run for both. The only workaround I found was to put the analysis job in a batch and then check for the last job run of the batch job against the target server, and from there get the analysis job run. From there its easy to generate the Remediation job and execute it to create the deploy job, but again there doesn't seem to be an easy way to get from the Remediation job to the deploy jobs you generate.
If your remediation jobs are actually running automatically you could probably just set up a nsh script job to query the progress of the deploy job run and sleep for a few seconds in between loops.