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It sounds like you're operating on large data that's in a custom C structure. To that end like with c++ I would recommend using the best linear math library for your datatype. And you can just query tf2 for the transform and then convert the transform value to your native type which will operate efficiently on your datatype without requiring a conversion.
The direct transform methods for messages and other specific datatypes like Eigen and KDL are designed as helper functions and are not necessary if you are working in some other system. Just use lookupTransform get the data out and use your C library for manipulating your data.
If you're ok with some latency you could implement a tf2 buffer client interface in pure C and query a remote tf2 buffer too. But I only recommend that when you know you are looking for a slow frequency query that's ok with larger latency.
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