I looked a bit into this today. I am using 3.49.2 specifically. On that release I see no way to disable rpaths. FYI: I posted a question in their forum https://sqlite.org/forum/forumpost/13cac3b565

 

ERROR: sqlite3-5_3.49.2-r0 do_package_qa: QA Issue: libsqlite3: /usr/lib/libsqlite3.so.3.49.2 contains probably-redundant RPATH /usr/lib [useless-rpaths]
ERROR: sqlite3-5_3.49.2-r0 do_package_qa: QA Issue: sqlite3: /usr/bin/sqlite3 contains probably-redundant RPATH /usr/lib [useless-rpaths]

 

After 3.49.1 the --disable-rpath option was removed which seems strange to me.