Yes. TrueProfit's Product Groups let you group products that should share the same shipping cost rules, layered on top of your shipping zones. Each group gets its own quantity-based or weight-based shipping cost table, so specific products (e.g. oversized or fragile items) can have different shipping costs than the rest of your catalog.
If multiple products from the same group appear in one order, you can turn on "ship all items together" so that the order isn't charged shipping cost multiple times for the same group.