Are you frickin serious?
VAT is only an actual cost for consumers. Yes, if you buy a Märklin model train for your son's birthday, you actually pay VAT on it. But businesses include in their VAT filings both the VAT they collect on their sales and the VAT they pay on their purchases, and pay the difference to HMRC (or get it back if the difference is negative). So VAT is never an actual cost for a business. When a UK rail company buys a train from a German manufacturer, it only pays the VAT on paper, and then immediately subtracts the "paid" VAT in its VAT filing so the net result is zero.
But what are we talking about British rail companies? British Rail is defunct, and most of the current operators are either owned by Abellio - a subsidiary of the Dutch railways - or by Arriva - a subsidiary of Deutsche Bahn - or by Eurostar, a subsidiary of the French and Belgian railways.
ETA:
No, the VAT rules are there to have unified VAT rules. VAT is basically a sales tax that costs the end consumer but whose administration runs through the whole value chain. And the principles of VAT are laid down in EU directives, notably the Sixth Directive, and those rule supreme over UK law. For businesses, VAT doesn't cost one iota, except for the administrative burden.