@Dbaca is this the document you're quoting? (page 10): https://ec.europa.eu/taxation_customs/system/files/2021-06/guidance_on_import_and_export_of_low_valu...
Because page 19 and 20 detail how to calculate the VAT 'tax base': the 'intrinsic value' plus the 'transport and insurance costs to the destination'.
Page 20 also includes a rather large table of examples which clearly have VAT applied to 'transport fees' as well as the cost of the goods.
Absolutely, you must make sure that you are shipping under the distance selling rules and IOSS. The EU intermediaries that you may have nominated for IOSS are a great source of information on what you can/can't do when shipping DDU/DDP/IOSS + or - €150 threshold. The rules are fairly black and white.
That the VAT taxable amount has not changed in not playing itself out. I really think that you should state - as the representative of an intermediary with clients reading this forum who may take your word as good advice - that you got that wrong. You confused intrinsic value with taxable amount. Own it.