All the variations of the logo and design mocks are clearly overkill for a $15k project. The design team had time to fill and wanted to provide lots of options for you to pick from, as they typically would on a larger project. Those variations are an expectation for $100k clients, and you got the $100k customer treatment, but unfortunately not at a discount.
The reality is, small jobs like this are effectively make-work projects for an agency. They typically don't pay enough to be an effective use of time for the agency, but are a way to stay in the black between higher value projects. Small customers become "nuisance" customers as soon as a something better is landed. The team members being swapped out as they are needed elsewhere and newly joining team members then need to re-contextualize and regain momentum, all on your dime.
Your takeaway is correct, don't be a small fish for an agency. If they're busy they won't take your work, and if do show interest, they are desperate for work.