I see your point there are two diagrams in the "02" HB 210.16 and 17.and they clearly show OCP for the secondary conductors. I do not believe they are installed for the transformer secondary.
But if you look at protecting the secondary conductors we would have to go to 240.21 (C)
240.21 (C) Transformer Secondary Conductors. It's opening paragrph follows
Conductors shall be permitted to be connected to a transformer secondary, without overcurrent protection at the secondary, as specified in 240.21(C)(1) through (6).
FPN: For overcurrent protection requirements for transformers, see 450.3.
(1) Protection by Primary Overcurrent Device. Conductors supplied by the secondary side of a single-phase transformer having a 2-wire (single-voltage) secondary,[text edited out]shall be permitted to be protected by overcurrent protection provided on the primary (supply) side of the transformer, provided this protection is in accordance with 450.3 and does not exceed the value determined by multiplying the secondary conductor ampacity by the secondary to primary transformer voltage ratio.
Your motor has a 40A FLC per 430.148. At 125% (430.22) you would need 50 Conductors to the motor.
The pri of a 3kVA trans draws 3/.208 = Approx 15 A.
The sec to pri ratio should be 208/240 = .86
If you multiply the 50 amp wire by .86 the answer is 43 A the 15 A pri fuse looks ok.
If you look at the figure in the 02 Handbook in article 450 page 572 exibit 450.6 it displays a autotransformer with out OCP on the secondary.
I hate it when this stuff happens!!
what do you think??