In accordance with embodiments of the present disclosure, a method may include, during boot of a modular information handling system disposed in a chassis configured to receive a plurality of modular information handling systems and a plurality of modular information handling resources, pausing execution of a basic input/output system. The method may also include communicating a first indicator, wherein the first indicator causes a chassis management controller of the chassis to perform link optimization operations of a communication link between the modular information handling system and a modular information handling resource. The method may further include, in response to communication by the chassis management controller of a second indicator, the second indicator indicating completion of link optimization operations by the chassis management controller, unpausing execution of the basic input/output system.