I think at the moment it's a little hit and miss, but if the buyer pays straight away (either through choice or through eBay forcing it) you won't be able to adjust anything at any stage, and eBay will either add up all of the individual postage charges and apply that, or apply any postage discounts you have in place, they won't do any calculations or adjustments themselves, only add what you've already input into the postage section (there are exceptions to this, eg some sellers have noted that automated postage discounts are applying to standard, but not a different service like express). I should note that this applies to the flat rate postage option, things may work differently with calculated postage or rate tables.
A lot of my buyers are not being asked to pay immediately, and are still able to just use the Buy It Now option on multiple items without going through checkout. When that happens, if they go to checkout without waiting for an invoice, it'll be the same as above (each postage cost is tallied, or if postage discounts are in place, the discount is applied), but I can also send a manual invoice and group the items together under a specified postage cost.
In some cases the buyer can make a single payment for items, but the seller will receive multiple payments - this is especially true if they buy and pay without a manual invoice, and there are different postage services selected for the items. eg If you have one set to 'Standard delivery' and one set to "Australia Post Parcel', even if the buyer checks out both items at the same time, postage discounts won't apply and two separate payments will be received by the seller. For this reason I have all of my default postage services set to 'Standard delivery' no matter what service is being used, so that eBay will keep them combined properly, and PayPal won't split single payments.
