Some applications contain boot time services. Some common examples of this may be SQL Server and Symantec Endpoint Protection, plus pretty much all popular anti-virus applications to name just a few. It's imperative for the SQL Services to start at boot time, if a user attempts to connect to a database on the SQL Server and the service has not been started, it will fail:
If it's something like Anti-Virus, you of course want your anti-virus service running and monitoring your desktop from the moment it starts. There's some applications that install services which by default appear to be set as Automatic, meaning they start automatically when the machine boots up or possibly Automatic (Delayed) which starts the service shortly after boot up. But when you get down to brass tax, you may discover the application doesn't actually require the services to be set to Automatic or Automatic (Delayed), setting the service to manual, allowing the service to start on demand, as required will suffice. (Services can be found under Control Panel --> Administrative Tools)
If your application does require to truly start at boot time. It's possibly to leave the service set as Automatic and have the application placed in startup or script the launch for login. I had to do something similar to this with App-V 4.6 in the past and never liked the experience. The application startup seemed to take quite some time, so the end user experience wasn't great. In App-V 5.0 with SP2 hotfix 4, SP3 or later , the performance is at a point that this may be an acceptable path forward for you.
The graph shows that if you have an application with Boot time services your best course of action is to try setting the service to manual during your sequencing i.e. launch services whilst sequencing and change the startup type to manual. If the application does not work as expected or desired and it's required at startup, leave the startup type as Automatic and place the application in startup. If the placing the application in startup is not acceptable due to packaging standards or performance concerns and the service cannot be set to manual you will need to deploy as a traditional install. Otherwise, go ahead and sequence!