The simple answer is yes an Employer is free to amend a standard nec3 contract. What must be remembered is that the standard contract has been set up to allocate risk between the Parties to a contract via use of compensation events.
If the risk is transferred to the Contractor you need to consider if he is in a position to control/mitigate that risk? Also if you allocate 60.1(12) to the Contractor he will Price for this risk in his tender and as an Employer you pay for this risk whether the risk occurs or not.
So for example a Employer gets an Optional Price from a Contractor at the time of tender for excluding clause 60.1(12). The Employer takes up this option - no risks materialise and the Contractor makes an additional profit by being prepared to take the risk.