It would help us to better and more specifically answer your questions if we knew which Kaspersky product (KAV/KIS/KTS) and which version (2016 or 2017)...
...but, generally speaking:
1) Yes, I suggest that you leave it enabled. The default settings are a balance between protection and performance. The "Advanced Disinfection" technology is proprietary, so there is not alot out there about it. But, unless you have an older system with old, slow hardware, it's best to leave that setting enabled. On a modern system with decent hardware, one should not notice any performance impact from leaving that default setting enabled.
Here is one article about the feature (from an ENTERPRISE product version support page) that explains a bit about it:
2) Yes. Having said that, most of the AVs are not very strong when it comes to detecting PUPs (or zero-day/zero-hour malware, either). The anti-malware programs, such as MBAM Premium, are better in those niches. That's why many security experts and advanced home users follow a "best practice" of running real-time anti-malware protection alongside their AV.
3) There is no one "best" AV that suits all computers, users, or budgets. The AV comparatives must be taken in context and with a grain of salt. My own personal observation as a frequent visitor at several security fora is that BD seems to suffer from more than its share of false positives, compatibility problems with other security apps (especially Malwarebytes Anti-Malware) and perhaps other issues. But that is only my subjective opinion based on my own observation of reports at computer support sites. Having said that, no AV is perfect and BD is probably as fine a choice as any other AV.