Transport agents not installing properly

We have couple of transport agents that were developed in house that we use in in Exchange 2007. When we installed them on test 2013 Exchange servers they installed and worked fine on one of them. On the others they appeared to install  properly and show in the list when we run Get-Transport agent. However, they don't do anything.

We determined that they were not being added to the agents.config file. Since this is a test environment we manually added the entries from the working server to the agents.config on the non-working server and everything now works perfectly. However, my concern going forward is that according to this article... https://msdn.microsoft.com/en-us/library/office/bb799630%28v=exchg.150%29.aspx... it is unsupported to manually edit that file.

Here is the contents of the agents.config file after editing it with the additions highlighted:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
  <mexRuntime>
    <monitoring>
      <agentExecution timeLimitInMilliseconds="90000" />
    </monitoring>
    <agentList>
      <agent name="Transport Rule Agent" baseType="Microsoft.Exchange.Data.Transport.Routing.RoutingAgent" classFactory="Microsoft.Exchange.MessagingPolicies.TransportRuleAgent.TransportRuleAgentFactory" assemblyPath="C:\Program Files\Microsoft\Exchange Server\V15\TransportRoles\agents\Rule\Microsoft.Exchange.MessagingPolicies.TransportRuleAgent.dll" enabled="true" />
      <agent name="Malware Agent" baseType="Microsoft.Exchange.Data.Transport.Routing.RoutingAgent" classFactory="Microsoft.Exchange.Transport.Agent.Malware.MalwareAgentFactory" assemblyPath="C:\Program Files\Microsoft\Exchange Server\V15\TransportRoles\agents\Antimalware\Microsoft.Exchange.Transport.Agent.Malware.dll" enabled="true" />
      <agent name="Text Messaging Routing Agent" baseType="Microsoft.Exchange.Data.Transport.Routing.RoutingAgent" classFactory="Microsoft.Exchange.TextMessaging.MobileDriver.TextMessagingRoutingAgentFactory" assemblyPath="C:\Program Files\Microsoft\Exchange Server\V15\bin\Microsoft.Exchange.MobileDriver.dll" enabled="true" />
      <agent name="Text Messaging Delivery Agent" baseType="Microsoft.Exchange.Data.Transport.Delivery.DeliveryAgent" classFactory="Microsoft.Exchange.TextMessaging.MobileDriver.TextMessagingDeliveryAgentFactory" assemblyPath="C:\Program Files\Microsoft\Exchange Server\V15\bin\Microsoft.Exchange.MobileDriver.dll" enabled="true" />
      <agent name="System Probe Drop Smtp Agent" baseType="Microsoft.Exchange.Data.Transport.Smtp.SmtpReceiveAgent" classFactory="Microsoft.Exchange.Transport.Agent.SystemProbeDrop.SystemProbeDropSmtpAgentFactory" assemblyPath="C:\Program Files\Microsoft\Exchange Server\V15\TransportRoles\agents\SystemProbeDrop\Microsoft.Exchange.Transport.Agent.SystemProbeDrop.dll" enabled="true" />
      <agent name="System Probe Drop Routing Agent" baseType="Microsoft.Exchange.Data.Transport.Routing.RoutingAgent" classFactory="Microsoft.Exchange.Transport.Agent.SystemProbeDrop.SystemProbeDropRoutingAgentFactory" assemblyPath="C:\Program Files\Microsoft\Exchange Server\V15\TransportRoles\agents\SystemProbeDrop\Microsoft.Exchange.Transport.Agent.SystemProbeDrop.dll" enabled="true" />
      <agent name="Maverick Contact Management Transport Agent" baseType="Microsoft.Exchange.Data.Transport.Routing.RoutingAgent" classFactory="Maverick.ContactManagementTransportAgent.AgentFactory" assemblyPath="C:\Maverick\ContactManagementTransportAgent\Maverick.ContactManagementTransportAgent.dll" enabled="true" />
      <agent name="Maverick MailIn Transport Agent" baseType="Microsoft.Exchange.Data.Transport.Routing.RoutingAgent" classFactory="Maverick.Exchange.MailIn.RoutingAgentFactory" assemblyPath="C:\Maverick\MailIn\RoutingAgent\Maverick.Exchange.MailIn.dll" enabled="true" />
    </agentList>
    <settings />
  </mexRuntime>
</configuration>

My question is...since this is working perfectly after modifying the file should we be concerned that this was not officially supported? We don't see anything negative effects from it but is it possible that something could show up later?
And what might be preventing our installer from modifying this file as it should be?

Thanks

Kenny