Thanks @ Shri Padmanatham Ji for specifically pointing out Section 15(2)(c) where value of supply includes "incidental expenses, including commission and packing, charged by the supplier to the recipient of a supply and any amount charged for anything done by the supplier in respect of the supply of goods or services or both at the time of, or before delivery of goods or supply of services"
I agree that this Section 15 (2)(c) is also an important element to be considered while answering the query.
Querist has said that material is lifted from "Transporter godown". If there is 'storage & warehousing services' is also involved by same transporter, then, another dispute arise whether 'loading charges' will be part of of value of 'storage & warehousing services' OR 'GTA Services' u/s 15 (2) (c).
Besides, one also needs to decide whether & if 'loading charges' is part of composite supply of 'storage & warehousing services' OR 'GTA Services'.
Again, if 'loading charges' is part of composite supply where 'storage & warehousing services' is the principal supply by the same person (i.e. transporter), then, Section 15 (2) (c) will not apply while valuing 'GTA' services.
Summarising above, entire arrangement needs to be looked into holistically to determine type of supply, number of services provided by the transporter, value u/s 15 for each supply provided read with Section 8, forward charge / reverse charge etc. before one can answer the first part of the queries raised.
Having said all above, if you are eligible to avail ITC against taxes so paid under RCM & if the supplier is not charging any gst against loading charges, it is practically advisable to pay taxes under RCM on 'Transport & loading Charges' (i.e. both elements are treated as part of value of GTA services received) and to take ITC there-against.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.