Solution
All the functionalities available in the Development Environment (ADE) can be used in the Runtime Engine (RTE) in terms of logic, execution, and coding design patterns. There shouldn't be missing tools, add-ons or functions at least distributed by NI when using stand-alone applications running under the Runtime Engine. This means that the execution of an application should be the same using both approaches.
The big differences are related to the debugging tools, like the highlight execution, profile performance and memory, breakpoints, probes, and all the related to the creation, modifications, and testing capabilities to work on the application's code.
Note that while the LabVIEW Application Development Environment (ADE) runs as the process "labview.exe", the built Applications will run as a separate process called "<applicationName>.exe". This can generate unexpected behavior if the Application files are scanned by an anti-virus software.
To verify if this is the case, temporarily disable the anti-virus software and/or its scanning features, then restart your PC and inspect the application behavior again.