At the time of construction, trains had a somewhat smaller profile than to day. Engines were not much more than 12 feet (3.6 metres) over chimney and 8 feet (2.5 metres) wide. Carriages were rigid four or six wheelers, 25 - 30 feet (8 - 9 metres) long, 8 - 8 foot 6 inches (2.5 to 2.6 metres) wide, and about 11 foot 6 inches (3.5 metres) over the tops of the oil lamp cowls. Freight wagons were tiny, just 6, 8 or 10 ton capacity. So it would never occurred to the railway company, its engineers and the construction companies of the period to build anything larger. They weren't clairvoyants. But the railway today has to live with the consequences of the decisions made 130+ years ago. Or make (very) expensive modifications.The only suggestion I could come up with - and this is speculation not fact - is from the Widened Lines built cut and cover - not bored - tunnels. The height restriction seems to be along and either side of the centre line of vehicle roofs i.e. where todays OLE wire is and where yesterdays carriage roof ventilators were. Tunnels bored with TBMs are circular, tunnels dug manually seem to me to not have flat ceilings but arched. Those with a circular or arched cross section are naturally higher above the centre line, room to squeeze in OLE for example. A cut and cover tunnel may have just been roofed over to clear vehicle height, but leaving it without that little bit extra clearance than an arched or circular tunnel would have. But this is all guess.
Take a look at this Met Carriage from 1892
Railway vehicle; Metropolitan Railway 'Jubilee' carriage No. 353, 1892 | London Transport Museum
railway vehicle