To be honest, that's still in the air. The answer really depends on how mod users take to it. Myrddraal's scripts in the beginning used the F1 method because it was a useful method for beta-testing, it could be activated but equally it wasn't so obstrusive that it would get in the way. It was there if you knew what you were doing. Because other modders have been using his multiple turn script, they've also transposed the F1 method.

I know that EB, we're aware that many of the mod users won't be big modders themselves and it won't necessarily be easy for them to get into the routine of the whole "Press f1, press request advice, press show_me" routine every time they reload, so we've looked into integrating it more naturally, so when they reload they'll be prompted to start the script when clicking on a HUD element or a settlement or the like. Now, that wasn't straightforward to implement, but it was our opinion that it was more in line with that mod's intended wide appeal.

There have been very few major mods released that have had an integrated background script to date (I think TFT, I'm not sure of any others) and that I think was an optional four turn addition.

After a few major mods are released a community standard will develop, as the mod users will get used to a particular method, right at the moment though, it's a compromise between ease of implementation for the modder and the ease by which the mod-user will be reminded of the requirement to reactivate.

Of course the new Reload event that Guy put into the BI release might change all that for mods intended for BI. We'll have to see how it operates.