Botrk doesn't make your W do more damage, it's just another on-hit effect. Also I could probably recommend trading in runaans for wits end. It gives you atk speed but it also gives you bonus on-hit damage AND magic resist shredding debuff that really helps to hit hard since AP varus relies on his autos to stack blight so you will be auto attacking anyway.
I personally have not tested the new rageblade on varus yet, so I can't comment too much on that but i would imagine that it might be good on teamfights with a crowded enemy team (also unsure on how it interacts with runnan's extra bolts.)
Personally I prefer a nuke AP varus thatcan burst down squishies in 3-autos and an ult and can also shred down tanks with its amazing % max hp damage. The thing is you want to be able to burst people down in as few rotations as possible IMO because of cooldowns and having to auto-atk less. His ult has 100% ap scaling that can definitely reach 1k magic damage with nashor's, deathcap, and a zhonyas with other prefered ap items. I usually get around 20% max hp damage per blight stack, usually killing squishies with 3 autos and an ult. Tanks will also get shredded with 3 autos, E, 3 autos, Q. (damn man I miss DFG....) or leave them close to dead while wondering where the hell their hp went.
Also note that since siege minions have negative magic resist, AP varus can easily kill them with 3 autos and a proc with decent ap. This makes him extremely potent at defending base when inhibitors are down. Note also that due to requiring blight stacks to proc his burst damage that it's usually a decent idea to have some sort of defensive plan built into his items (Usually, though not required. Just a contingency plan usually saved for enemy team's adc or other bursty champ) to make sure he lives to get his procs off.
the one downside I feel that AP varus has is that he doesn't have quite as strong lane presence since his Q doesn't scale with ap and that's a pretty big part of his kit in laning and trading/harassing.