Bast's link to Sekhmet is usually due to the Upper and Lower Egypt duality between them, and sometimes they are erroneously referred to as sisters because of their similarities and this fact. The ladies are similar in that Bast and Sekhmet both represent the heat of the desert and of the land of Kemet (Egypt), as well as both are Eyes of Re (and/or daughters of Re), and they both have feline heads.
However, Bast is a netjer of gentle heat, while Sekhmet is a netjer of destroying heat. Bast is a cat goddess, while Sekhmet is a lioness goddess. Bast, yes, can be extremely violent, especially against causers and allies of isfet. However, she is mostly viewed as a mothering netjer, even in ancient Kemet.
Hetheru (Hathor) is linked to Sekhmet through a story of Sekhmet's near destruction of the world, where Hetheru turns into Sekhmet to destroy humanity, then gets drunk and turns back into Hetheru, then gets miffed when she sobers up and finds her honor destroyed, runs away into the desert (becoming Sekhmet once more), then turning back into Hetheru when she is convinced back to Kemet.
A mother is not just nice, pretty, and lovely. She's also violent when her babies are in trouble, and strict when they are being stupid. Mothers are blessings in disguise often, as they are often "annoying, mean, and nasty"; however this is usually to how much they love and care for us. Bast is the same in this.
Bast's worship in ancient Kemet wasn't always lovely and nice, and many books on Kemet will make it seem like they were perfect little people who made emphasis on purity and kindness and all that. They weren't. Bast's worship sometimes involved the ritual strangling or drowning of cats that were then dedicated to her, or sent to the afterlife with messages from the living to the netjeru. I'm not mentioning this to gross anyone out, offend anyone, or disgust them. I'm bringing it up to drive home the point that she isn't perfect, just like the rest of the netjeru, and that she (and her offerings/sacrifices) can often be violent-natured.
While Bast is not my patron (and I do not have any particular netjeru or other deities as my patron [s] ), I have spent a particular amount of time studying ancient Kemet, their customs, and their culture.
Also, if I remember correctly, Apophis is the name of a foreign ruler of Kemet during the Hyklos phase, that was later adopted as the Greek name for Apep. Apep, while an ally of isfet, is not a great evil, but more or less a neutral being that is destructive by his own nature (much like Fenrir of the Heathen pantheon). He has to do what he was born to do, or else it would not be in his nature. Often, he is left unmentioned by name, or his name is broken up, images of him are being attacked or destroyed when they are shown. It is for protection from him and from the wickness he does, otherwise his images or name may come to life and destroy as he would.
I'm not saying I love Apep, I just don't consider him a truly evil being. That doesn't mean I feel that the rituals for destroying Apep and his power aren't necessary; I like that the sun continues to rise in the sky. ;)
Sorry for ranting so much, but I'm an odd ball. :)