Fascinating thread. All protocol has its roots in tradition, and there's scarcely a tradition that is practiced from time immemorial.
Politeness, etiquette and politesse probably overlap with protocol, but protocol is closer to the word "regulations" than it is to the word "etiquette." The word itself doesn't enter English until the 16th century, and comes from the Latin, where its first use of course, had nothing to do with Catholicism. The Romans took the word from the Greek s(protokollan, original glue.
So protocoli change over time, which is why I personally find the study of both protocol and etiquette so interesting. I do not think wearing a long skirt to a morning wedding is a breach of protocol, but it is a breach of standard Euro-American etiquette. Etiquette (a French word, of course) comes into English later than protocoli. Etiquette is highly standardized in Europe by the early 19th century, which is probably when the wedding dress rules were formalized, although those rules are based on earlier ones. I can't remember when it was (during the Renaissance) that wearing white at weddings become popular, but I believe it was Italian Renaissance princesses/duchesses who popularized it (previously, black had been the color in many places; Eastern Europe often had a different code of color for events). It's fascinating just to think about how white has caught on as the official or preferred color for wedding dresses - relatively recently (and of course, not everywhere).
All cultures have etiquette of course, whether they have the word or not, but to me the word today means a specific system, which forbids wearing of certain garments at certain times of the day, if one is to be proper. I don't think such rules are ever supposed to be put on the wedding invitations, myself!
Protocol is, according to most standard definitions, internationally agreed upon etiquette for use in diplomatic situations. Diplomats, heads of state and others are supposed to know and follow it, but I wonder if Queen Rania really has an on-staff expert on Western protocol.
I believe that if royals and others don't follow protocol and etiquette, their status is diminished, and probably more so than by almost anything else they might do. Naturally, younger royals aren't forever besmirched by breaches, but older royals really do have to teach and model the rules (it seems there are so many).
If a senior royal decides to modify a rule of etiquette (or even protocol), that's precisely how etiquette changes. Future monarchs either will or won't bow/curtsy at funeral corteges of those who are not monarchs; there will probably be opportunities to observe this in our lifetimes.
I believe that protocol changes only when heads of more than one state agree upon it, but that may be the personal spin I put on the word.
And, since we have no reigning royals in the countries where I spend most of my time, let me add that heads of state are not merely royals - but they should follow protocol as well.
And have manners.
According to Pikul, Dowager Empress Maria Fedorovna attended the coronation ceremony of Nicholas II, but she never bowed/paid obeisance to her son. 
