What I don't understand is why gear guides aim for 40% cap purely through armour alone and don't consider traits or merits.
Because the job trait MB Bonus isn't subject to the cap.
The AM merits, yes, but element-depending, those generally fall somewhere between a tier 4 and tier 5 spell (though at some select dINT levels, they can be stronger than a tier 5). If you're magic haste capped (which you ideally would be for anything challenging), your cooldowns are low enough to never need to go past the tier 5, tier 6, and -ja spells, unless the skillchains are really flowing. That plus magic bursting has fallen out of meta favor, so in general there's not as much incentive to min/max an AM2 set. Ongo is a recent exception to this, where Quake 2 gets use.