Everything that existed in 1965/6 would have been allocated a class number. Shunters of different builds were grouped, such as in class 05. He did say they were gaps in the DML numbers for possible future builds.
Intriguing - so as well as 10001 (withdrawn 1966) this brings several shunter classes into scope (Data from "Diesel & Electric register, by Andy Chard: corrections welcome): unless stated all tghesed classes went extinct in 1967
D2400 etc - Class D2/5 Barclay 0-6-0 (same 204hp Gardner engine as classes 03-06: note that the Barclay Class 06 was an 0-4-0) extinct 1969
D2500 etc - Class D2/7 Hudswell Clarke 0-6-0 (same engine as classes 03-06) - end cab
D2510 etc - Class D2/12 Hudswell Clarke 0-6-0 (same engine as classes 03-06) - centre cab
D2700 etc - Class D2/1 North British 0-4-0 diesel hydraulic (Paxnan 200hp) extinct 1968
D2708 etc - class D2/10 North British 0-4-0 diesel hydraulic (MAN 225hp) extinct 1968
D2900 etc - Class D3/1 North British 0-4-0 diesel hydraulic (MAN 330hp)
D2950 etc - Class D1/1 Hunslet 0-4-0 (same 153hp Gardner engine as the Barclay Class 01)
D2957 etc - Class D1/3 Ruston 0-4-0 (Rustion 165hp) extinct 1968
D2999 - Class D2/11 one-off Beyer Peacock/Brush 0-4-0 diesel electric (National of 200hp)
D3117 etc - Class 3/3 Crossley-engined variant of Classes 08/10:
D3152 etc - Class 3/5 Variant of Class 10 with BTH electrics:
12003 etc - Class D3/7 LMS design with jackshaft drive:
15000 etc - Class D3/9 LNER design,
15100 etc - Class D3/10 and D3/11: GWR designs
Even if you group classes with the same engine, wheel arrangment and transmission together (and that includes what became classes 03-05) you have fifteen classes to fit where there was only space for twelve.
For completeness, the other pre-TOPS shunter classes are as follows
D1/2 - Class 01
D1/4 - Class 02
D2/2- Class 03
D2/3 - ?
D2/4 - Class 04 (D2200-14)
D2/6 - Class 06
D2/8 - Class 05 (D2550-2573)
D2/9 - Class 05 (D2574-2618 - none of these received TOPS numbers as they were all withdrawn by 1968)
D2/13 - Class 04 (D2215-2341)
D3/2 - Class 08 and 09
D3/4 - Class 10
D3/6 - 12000 etc LMS 1936 design: all withdrawn by 1962
D3/8 - Class 11
D3/12 - SR design 15201 etc all withdrawn 1964
D3/13 - Class 12
D3/14 - 15004 LNER design with Brush engine, withdrawn 1962