Lack of consistent samples is not an issue with professional use of MIDI.
Professionals (musicians, engineers, etc) don't use MIDI as a general-purpose playback method, they use it to control their samplers, synths, external effects units etc.
They don't need "consistent samples" because they provide their own samples, different for every song (plus pure synth sounds, etc).
This is going to be hard to explain without outlining a whole recording setup, but basically, a lot of the time, in a given musician's studio, the program numbers are going to refer to different things depending on how he chose to configure the patches (presets) on his synthesisers. In some cases, patches aren't even used, such as when an old Minimoog is retrofitted with MIDI and the notion of "Flute" or "Piano" becomes meaningless. In other cases, the synthesiser is a sampler and the samples were programmed by the musician at custom program numbers. In the case of software instruments in a DAW, patches are usually chosen by the DAW itself and no program message is sent to the synth, just note on/off, modulation, pitch bend and other controller messages, and if a switch of instruments is needed during a song, you just add a new track for that.
Basically, MIDI began as a protocol used between hardware devices. General MIDI is a product of the ROMpler era, a ROMpler being a sampler that can't be reprogrammed, i.e. what most people know as a "keyboard", and it's far from universal.
Musicians often don't care about standardising. They're hooking up all sorts of wonky instruments to their rig and reconfiguring it for one-off projects. There is often no need to recall specific patches after you've recorded the part you wanted.
