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How can I load lots of data at a time with Aidbox API?

You can use Bulk API for that

How to increase speed/performance for requests with complex parameters?

Create indexes for that.

Does Aidbox support 2-factor authentication?

Yes, please, check out the documentation.

How to create a SearchParameter for extensions on a property in a resource?

You can create custom search parameter for extensions and to made SearchParameter easier to write you also can define attribute

I’m building a request with revinclude. Is it possible to also apply a search for the include resource in that request?

In the FHIR Search API this is called chained-parameters. Read the details here and here

Aidbox appears to have a POST size limit of 20 MB by default. Is this configurable?

For sizable data, we recommend using Bulk API

I don't want to use BASIC authentication for security reasons. What can I use instead?

We suggest OAuth implementation in Client Credentials Grant. You need to use “Client Credentials Grant + Access Policy”:
An example of the query that doesn't work:
GET /DocumentReference?patient=
It’s called an absolute reference. Aidbox doesn't work with absolute references because the logic can become very tricky since these references can point to external servers.
Use relative references instead: GET /DocumentReference?patient=Patient/1234