The shipping cost of each part received on a PO will track to the work order.
EBIS will do this and the process is pretty much the same as in 3.2 -- you must do this in the receiving process. For example:
In P/O 3957, you can see that there was shipping set during the receiving process.
This was applied to the W/O at the part level and can be found here:
One thing to remember is to enter the shipping fee in the P/O > Config & Info screen before receiving the parts. EBIS will then recommend the shipping fees for each part accordingly (based on various city options). Normally, the shipping is distributed based on the % of the total P/O amount for non-inventory items (as typically shipping isn't tracked separately into stock, although you can enable this from Config > Lists > Stock Rooms and set the "Track Ship Fees for Stock" checkbox (turn the boxes green). Then, when receiving in parts, it should allow you to carry the shipping fees into the stock quantity at a per qty/unit level, and this can then carry over to a work order once it is pulled from inventory.
Note that there are additional shipping options in your city setup > Options > Purchase Order section > Options such as "Shipping: Recommend shipping costs for parts on P/O" and "Shipping: Include stock destinations in recommended shipping costs for parts". If setting stock rooms to track shipping, these various city shipping options are normally set also.