In the PHB we have the following rules concerning a size difference of two or more:
- You cannot move through a hostile creature's space unless it is two or more sizes bigger than you. (PHB 191, Player's Basic Rules 71)
- You can drag or carry a grappled creature but your speed is halved unless the creature is two or more sizes smaller than you. (PHB 195)
But no automatic advantage or disadvantage based on size.
NB Small creatures do attack at disadvantage when wielding heavy weapons (PHB 147, Basic Rules 46), but that is because of their size and the weapon's property, not the relative size of the opponent.
The issues you might have
This is written assuming you go for method 1 or 3, or you go for method 2 and the players roll a good set of stats. Personally, I'd avoid method 2, since it has a lot of ways to go wrong that nobody would be happy with; if you want to give them a powerful array, just let them have one that you decide on, and then you know what level they're on.
Increased power level
In general, letting the PCs have higher stats like this - and all of your proposed methods let them potentially start with an 18, assuming an appropriate race - allows the PCs to have about a +1 to hit and a +1 to damage. This makes them a bit over 5% stronger offensively, and probably another 5-10% stronger defensively because of increased saves and hit points. This probably equates to about .5 of a CR in terms of how challenging encounters will be.
Skill check DCs are by comparison easy to adjust - just expect your players to always get 1 higher than average characters of equivalent level.
Flatter top end
If everyone is special, nobody is. That is to say, if everyone gets to start with an 18 in the stat that they care about, it's not nearly as special when somebody reaches 20. Bear in mind that the items and abilities that set your ability scored are designed with "standard" player characters in mind, so a wild-shaping druid may feel underwhelming since their wild shapes are less effective than other players, and items like the amulet of health are less wondrous.
Feats everywhere
With the need for ASICs to be spent on stats massively reduced, your players will definitely want to take more feats. Some feats (such as Sharpshooter) are massively beneficial in combat, sufficiently so that if they play things smart they might be hitting a full CR above their level.
So what do I do?
There are a few paths; feel free to mix and match from these options as well.
Adjust the world upwards
The most obvious option is just to deal with it by making things a little harder. You'll probably have to adjust monsters upward occasionally - tweak a few monsters by giving them a unique description and bumping their attacks or defences up by a point, and maybe an extra HD or so.
I'd advise being clear with your players that they're building powerful characters and that you plan to challenge them appropriately from the start.
Let it roll
Specifically, let the players be slightly overpowered. D&D is already positioned for the players to be the heroes overcoming evil; they'll have a slightly easier time of it than most, but they may well enjoy that. You may find this frustrating as a GM if your encounters have difficulty challenging them, but a difference of +/- 1 shouldn't be that bad.
Reset expectations
Tell your players that you want to run a campaign at the standard power level. Make it clear that they're not expected to have or need "optimal" ability scores, and that the standard array/standard point buy will not impede their ability to be adventurers.
Best Answer
The Storm Rune's Prophetic State lasts for one minute and you can use the reaction multiple times in that minute
The Storm Rune states (emphasis mine)
What invoking the Rune does, is it sends you into a prophetic state for 1 minute. You grant yourself a buff that lasts for one minute. The description does not state any way for the state to end other than being incapacitated or the minute running up; so those are the only ways for it to end. For the entire duration of this state, the full minute, you can use your reaction in the new way described.
If using your reaction ended the state, it would explicitly say so. The thing you can't do is enter this minute-long state multiple times per short or long rest, which is what the final sentence is about. It isn't saying you can't use the reaction multiple times, it's saying you can't invoke the rune multiple times. What invoking the rune does is enter you into the prophetic state; using the reaction is not invoking the rune so it can be done freely.
The fire, frost, and hill runes all have a somewhat similar effect of granting a buff that lasts over time. Benefitting from those buffs does not count as invoking a rune, the buffs simply last for their duration. Invoking a rune is what starts the buff.