Can a wholly owned subsidiary have different benefits from the main corporation?

As a general rule, yes.

But you can run into trouble quickly, if the parent company has a disproportionate number of "highly compensated employees," due to various "nondiscrimination" requirements in the Internal Revenue Code.

Which benefit programs would the parent company be providing that are not provided on the same terms to employees of the subsidiary?

Health benefits. The parent company pays the employees' cost of health benefits only, which are specific to Reno, NV. The subsidiary (which has not yet been acquired) pays for employees' health benefits and also pays 100% of the cost to insure spouses and dependents. Since the potential subsidiary has offices in different parts of the country, their benefits would be more regional (e.g., Blue Cross Blue Shield).