In computer environment you don't really have the variables of electronics because they are so precise given how expensive components are, they are buy-able because of mass-production. I also think abstraction on application level would play some role in sound being accurate. On top of this sound is generated by VCV rack I think? And not a discrete CODEC chosen by the module designer.
In a physical module, for example Plaits, an ARM Cortex core microcontroller is used with a ciruit that surrounds it. Resistors are 1% meaning they have 1% max offset value, although each module is calibrated then you have the i/o from a CODEC and/or DAC, ADC. Given the modules are engineered according to these specific components, it's normal they sound different in an application.

Take all this with a grain of salt though, I am an embedded engineer, not really into higher level applications. So I am just making this all up lol.