Not sure with TBC 2.6.2, but it's a new feature of TBC 3.0 Beta 1:

- Feature: If "run query on base model" is activated then
AllegroGraph's native SPARQL engine will be used

Source: http://www.topquadrant.com/topbraid/composer/changes-3.0.0.txt

Query Processing on the base model

The option Run on base model only can have a dramatic impact on the
query performance when the underlying triple store provides native
SPARQL optimizations. For example, Oracle 11g and AllegroGraph come
with their own low-level SPARQL processor and this may have
significantly better performance than running a query in the default
mode (in which it will be entirely handled by Jena only and involve
several round-trips to the database server). If activated, the query
will only operate on the base model and therefore not see any system
triples, imported triples or inferred triples (except those natively
inferred by the databases). Neither will the uncommitted changes be
visible, because they are only stored in an in-memory graph by
TopBraid but not in the database yet. Also note that the expressivity
of a native SPARQL engine may be different than what is offered by
TopBraid's built-in Jena engine. For example, OPTIONAL patterns may
not be supported on all native engines. Also, SPARQL extension
functions will not be visible.

Source: SPARQL View help

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