Does the order of exercising a specific muscle first in a split routine matters? For instance, in a chest/back, shoulders/legs or biceps/triceps routine, does exercising a specific muscle first matter (like chest BEFORE back) or can they be alternated in the next workout since for example, chest and back train independent of each other?
Difficult question. If you go through the book "supertraining", you will notice that each parameter you change can have an effect on your training and its outcome (moment you do the iso-hold, speed at which you train, including bodyweight after heavy strength, ...).
You can easily imagine that you are fatiguing some muscles when doing one exercise. In a superset, it is probable that the second exercise will be affected by the first one (this could be the intent : fatiguing some muscles in a first exercise to make sure you are using some other specific muscles in the second exercise) and maybe you will compensate in some way, ...
So to have a well-balanced training and because it is impossible to quantify/assess every training parameter and outcome, mix it up as you suggest. Switch regularly the first and second exercise in a superset, for example.
Well-designed variation is key to avoid compensations, imbalances and injuries