I'm not sure about your questions, but mixing runes is very situational, imo. Generally, I'll keep up one type of Rune if I know a boss focuses on one type of damage; if I were to take it to Delve, for example (hypothetical, I haven't done so yet!) I'd use Unda against Tojil, Sulpor against the shark, etc. However, against targets that use multiple elemental abilities, I'll generally keep up two types of runes. An example I can use from earlier on is when I used to solo Tapana in WoE Flux... 11, I think? Either way, he's very fond of ice-elemental magic (Blizzaga IV particularly) as well as Paralyga. However, he also uses Blindga and some of his TP moves are dark-element (as I discovered when I accidentally absorbed a Raksha: Vengeance) so I'll keep up one Dark rune to resist Blindga a bit more easily as well as being able to toss up a Liement for either element for a quick absorb, should I choose it.

For the most part, you'll generally stick to one type of Rune, but there are niche situations to using multiple runes. The reason you want to stick to one is because the three resistance boosts stack together to give you a much higher one, increasing your elemental resistance to that element significantly. If you use another rune, your first resistance is cut by 1/3, making you less likely to resist. So it's not often a good idea to mix rune types unless you know you're going to do a quick defensive ability to complement it.

As for your two points... I'm not sure what you're asking about in 1); what do you mean they're not applied simultaneously? Like, in their usage? It's a JA that has a cooldown, nothing more. As for 2), you don't need to have the dancer finishing moves thing because you can only have three runes active and you have one symbol for each you have active, even if they're the same type. You could have three Unda buffs up, which means three Unda Runes are active, and a new rune will overwrite the oldest.

As for swapping all at once, I wouldn't complain. XD; I'd like that.