I may have mis-understood your question, if the issue only with a mode change then yes it could be addressed by an app or DTH modification (depending on how its setup) and probably not related to the device or mesh.
You may not even need a virtual thermostat if you’re using climate SmartApps which support remote sensors and switches to control heaters/coolers natively. Here are a few smartapps from RBoy Apps which support remote sensors/switches to manage climate and do take into account mode changes:
[RELEASE] 5-2 Day Programmable Thermostat Scheduler (Weekday, Weekend) with Remote Temperature Sensor for each Schedule
[RELEASE] Mode Based Thermostat - Control Multiple Thermostats Temperature / Remote Temperature Sensors when Changing Modes
[RELEASE] Motion Sensor Thermostat with Remote temperature sensors, Presence detection and Schedules