Looks like it involves VcHostAutoStartManagerConfig API Reference and powerinfo API Reference if changing the startup order @ host level as long as you're not in a HA cluster
I remembered vApps support start order as well VcVAppConfigSpec API Reference and VcVAppEntityConfigInfo API Reference which sidesteps the issue of startup sequence for vm's at the workflow level but might add complexity elsewhere dealing wiht mixes of vm's and vApps
Other option would be as you say to use custom properties to set a start order priority for every vm across the environment.
My coding/scripting skills aren't at a level to phrase this correctly but would it be possible to re-use existing objects, attributes, scripting classes to reproduce similar features with startup order, startup delay, stop order, stop delay and stop action but store the values in custom properties?