Re: Cost is the smaller concern
Depends what they modify... Most installs of anything are customised to some degree, and these customisations have to be adapted to future versions.
If they're making significant changes (e.g. the addition of smartcard support) they could commit these back upstream, so future versions have the support by default.
Of course for an organisation the size of the NHS, where so many users have very similar needs the cost of customisation could easily be outweighed by the benefits of software more tailored to the needs of the organisation.