If this is part of RFP, this paragraph is addressing the evaluation of the cost proposal submitted which contains errors due to the deviation of the requirements/condition applied in the calculation of the cost. the example cited is to show the consequence of such error in implementing the contract.

Any deviation from this condition will be loaded accordingly for the purpose of evaluation.
loaded, a contract term for calculated, computed
deviation of condition, the use of elements/conditions/requirements not stipulated in the RFP.
the evaluation is based on recalculated amount by the evaluators. Two things could happen: the proposed cost could be very low, to the detriment of the bidder, or the cost could be high, which makes the cost proposal non-competitive.

i.e. the Owner shall load maximum penalty under penalty for late delivery Clause.

This seems to indicate that the condition (requirement) is a variable affecting the contract delivery, hence the penalty clause. Sometime the deviation itself is minor and does not affect the profit too much, but the risk factor is greater than anticipated/tolerated by the bidder.

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