Moodle already solves difficult learning problems
Courses, question banks, completion, users, roles, grades and a mature plugin ecosystem are expensive capabilities to recreate. If those functions fit the product, Moodle can provide a strong core.
The default experience does not have to define the product
A custom theme, dashboards, APIs, mobile applications, enrollment flows, reporting and external commerce can sit around Moodle while the LMS continues to handle learning records.
Custom makes sense when the product itself is the differentiator
If the learning model, user experience, business model or workflow is fundamentally different from a traditional LMS, a custom platform may reduce long-term friction.
Hybrid architectures are often the strongest choice
We have used Moodle as the learning engine while custom APIs and mobile apps delivered a purpose-built student experience. That avoids rebuilding mature learning infrastructure while still giving the product room to feel unique.