Overcapping is an issue on any job with a resource meter, so I'm not sure why anyone would present this as a unique issue on DRK. The risk of overcapping is reduced when you have a bigger capacity relative to the cost. Having dead space on your meter just locks down resources for no good reason. Your functional capacity is still the same. If the 200 MP/tick is worrying you, then get rid of it.

Edge and Flood cannot create double weaves on their own, because they have a 1s shared recast. Many jobs, including GNB, RPR, SAM, and NIN utilize this 1s recast to prevent double weaving the ability with itself. In fact, even if you took away Edge and Flood altogether, you would still have plenty of double weaves.

If you want to reduce the number of double weaves, then you need to incentivize spreading them out. On RPR, for example, all your Soul spenders generate Soul Reaver stacks. So while you could in theory double weave Blood Stalk with Gluttony, you never want to, because you override the stacks. You could do something similar by having attacks like Shadowbringer and C+S/Abyssal Drain cost MP but generate blood in return. Or you could redesign the Dark Arts system around this.

Plunge is another unnecessary culprit for weaves. Melee DPS have moved away from gap closers that are damage gated. I'm not sure why this isn't the standard now on tanks as well. You should be allowed to use your movement tool as a movement tool.

It's also worth noting that both GCD length and weaves contribute to APM. You'd actually have a slightly higher APM with a 1.5s GCD and single weaves between every GCD than you would with a 2.5s GCD and double weaves between every GCD.