Burgess J.W. Raby & William L. Raby have published Asset Transfer to Joint Venture Incurs Golden Parachute Excise Tax, also available on the Tax Analysts web site as Doc 2006-212, 2006 TNT 3-26. Here is the Conclusion:

The golden parachute rules can apply in unexpected situations, as Yocum may have been surprised to discover. Some compensation agreements provide that regardless of the other provisions of the agreement, no payment will be made to the extent that it would constitute an excess parachute payment within the meaning of section 280G and thus thereby attempt to avoid both tax disallowance to the employer and excise tax to the employee. However, restricted stock agreements of the sort between Millennium and Yocum typically do not include such a provision.

Insertion of those clauses is not necessarily in the interests of the executive. The economics of a contract without such a savings clause almost always will be more advantageous than otherwise. To the employer, though, savings clauses are no-brainers. They avoid compensation disallowances (which otherwise would reduce income tax by, say, 35 percent) in favor of not having to pay the compensation at all.

A partial compromise may be to build up the base compensation on which the excess compensation is calculated. Outright payments in employer stock, for example, supplemented by cash bonuses sufficient to pay the tax on the total of the stock and the cash bonus, can build up the base compensation and justify a much greater amount of parachute payments on change of ownership or control before those payments hit the "excess" level.