Has anyone played with both of these pick ups? I really like the Mother's Milk but the 69 CSs aren't bad either and are about 100$ less. I'm looking for a blues / alt rock / heavy blues type of sound (Buddy Guy, Frusciante, Dan Auerbach). Would either serve me well? Thanks.

My Gear:
Guitars: Vintage LP, Martin DX-1, Epi Viola Bass,
Amps: Marshall JMD501
Effects: Empty Set right now
For what you want, with fender p/ups, I'd recommend 57/62's, or CS54's. The 69's have a bit of a scoop in them, and I think the more vintage style p/ups will get you closer to the sounds you're after.
The 57/62 set is more what you would want from fender, not the 69? The 69 is known for it's Hendrix like midrange quack while the 62 is known for it's warm smooth midrange and lows and a crisp high end chime.

If you go BKP then you will want the Apache set which still uses the formvar wire (most important) but also uses alnico 3 magnets which gives you a thicker pre production 1954 strat sound.

Ideally you want a formvar pickup with alnico 5 magnets and it should be hand wound. The fender and BKP neither one make anything exactly in those specs but if you special ordered an apache set from BKP and asked for alnico 5 magnets I'm sure he would do that for you. Then there is always my smooth groove 62 set which actually uses the correct wire, magnets bobbins, AND its hand wound all as standard.
Not taking any online orders.