MFA enable/disable: there are multiple places and methods to enforce MFA for users in a Microsoft tenant. So yeah, it can be disabled in one place, and enforced in another place. For example, conditional access policies may require it while the older deprecated interface for enforcing MFA may show it as disabled. For better or worse, this is common to many topics in Microsoft-land, a combination of there being three different ways to accomplish the same thing (which is probably most often a feature, honestly), and the relatively rapid pace of change (a double-edged sword) that deprecates terminology, branding, and tooling frequently. It does require you to actively work to stay informed about how the platform evolves over about a 18-24mo period.
Payment History/Billing: It honestly does benefit most business customers to work through a Microsoft partner rather than a direct relationship, oddly enough. A partner will often have far more flexible license commitment terms, more flexible payment methods, occasionally have better pricing, and always have better invoicing and reporting capabilities than are offered in direct relationships. Microsoft's cryptic payment history and invoice reporting is pretty offensive - it works great as long as you never have any questions.
All that said, direct relationships are for customers that just need the basic services without any special requirements; partner relationships are for businesses that have more mature requirements but don't want to be experts on the rabbit hole that is Microsoft-land. Many SMB Microsoft customers attempt to go it alone thinking it's easy (in no small part due to MS marketing) but the minute a business wants to get more than ankle-deep in any technical domain such as endpoint management, data loss prevention, compliance management, threat management, etc., they will quickly find themselves underwater - not because it's complex (it's all easy) but because it requires a lot of deep-quirk knowledge and ongoing maintenance and monitoring. This isn't necessarily particular to Microsoft, though I think a lot of marketing has gone into creating the impression that IT can be 'easy'. But just like a IDS/IPS, buying the tool is the easiest step - it's the care and feeding that really saps your labor force and makes most solutions fail. Policies need to stay relevant, state need to be monitored, deviation needs to be remediated, changes need to be incorporated. It (IT) takes constant work to do it right.