As mentioned, the standalone version will be discontinued and only the source will be provided for running under Matlab. This is because the deployed version behaved slightly different than the source version, and ran much slower. So, going forward, development will not be halted by limitations of the deploytool.
One of the limiting issues of the deployed version was in parallel execution of the code. It ran fine in Matlab, but not when deployed. So now this feature has been re-implemented, as of Fatlab 2.022. It uses the Parallel Computing Toolbox. Fatlab will detect whether the toolbox is installed and enable it accordingly. The user can then select a number of cores for the execution under Run Analysis.
Special thanks to Martin Dahl Kilt for helping with this feature and performance issues.