The new payment system  has nothing to do with it.   When a person buys with whatever postage option you have set,  it is up to you to ship via that method, and it is up to you , where and how you source and pay for shipping.

If you decide to source postage via ebay, then you will incur postage costs at the time you generate a label and you will be charged according to what service you have selected during the label creation.  If you make an error and need to cancel a postage label, then you need to cancel the incorrect label within the stated time frame, 5 days I think and then wait at least 25 days for a refund.

Note the label system has been in place for years, long before managed payments was even thought of, but MP seems to cop the blame for just about anything.

By the way,  I would not recommend trying to negotiate  postage costs etc as you describe, as it may be interpreted as an attempt to avoid ebay fees which will result in your account, and also that of the buyer being terminated.