I'll answer your second question first. Unless your proprietary lease or house rules state otherwise, there is no reason why the buyer and seller can't work that out among themselves. The seller needs to be aware that there is a flip tax so they can discuss it with the purchaser. The final results of the negotiation are usually included in the Rider to the contract of sale.

As for if it is beneficial, I would say it is. Especially for a small co-op that does not have a large base over which to spread costs like capital improvements, it can be a way of increasing capital reserves. Just make sure your board attorney is involved with implementing a flip tax. There are a lot of rules which need to be followed, and if you don't have any enabling language in your governing documents, an amendment to your proprietary lease may be needed. There have also been a number of recent legal rulings regarding flip taxes, so your attorney is the best one to help.