It's not uncommon at all, but mostly with modern developments (last 20 years or so) where this type of clause was put in to fleece the future leaseholders. That's why the Government changed the law to stop the practice (but does not apply retrospectively).
A deed of variation would need to negotiated by the current leaseholder, not you as would-be buyer. They will have to pay the legal costs of the freeholder and also their own, plus negotiate a 'premium' to compensate for loss of future ground rent (and even go to a Tribunal if they can't agree this 'premium').
If its a problem for your lender then it's probably 'game over' on this particular flat due to a) the likelihood of the current leaseholder being willing to seek a variation and b) the time it could take.
However, if your lender will still go ahead without the deed of variation then, yes, you probably do need to consider what discount you should try and negotiate.
Depending on the level of ground rent (that is to double) and term remaining on the lease, the 'premium' for a deed of variation (e.g. to set a future peppercorn ground rent) could easily be in the high thousands or tens of thousands, plus your and the freeholders legal costs (you would pay both).
Whether the vendor agrees to 'any discount' is of course another matter.