The problem with Clapham Jn is that there are two completely separate major infrastructure projects on the table, but we only get one or the other, not both. If Crossrail 2 goes ahead, then additional calls by mainline services at Clapham Jn become feasible because of the additional paths made available because some trains will switch to the present main slows east of Wimbledon.
If Crossrail 2 doesn't happen, then the alternative is the 'Fifth Track' inbound from Surbiton to Clapham Jn, with a reversible main line between the up and down main. (Track layout details as per the 2011 London and SE RUS▸ .) That will also allow a number of main line services to call at Clapham Jn, at least in the peak flow direction.
Until they decide which of the two main solutions to implement, it doesn't surprise me that detail is hazy. But surely the choices are in the study, being described as post CP6▸ work within the options A,B and C on page 9?
I'm not entirely convinced by that. The timescale of Crossrail 2 must be long ... or longer still, so some reworking at Clapham might still be worth doing. It would probably be needed with the 5th track option in any case.
What may be more important is that it never was a capacity-enhancing change, more the opposite. So while the Route Studies start by summarising the cheaper interventions that add capacity, to see if more is still going to be needed, this one does not have to be included. However, given its prominence last time around, it still merits being mentioned to say why it's not being considered this time. Of course the reason may be "we can't find a cheap simple way to do it" - i.e. every time we try to work one out it evolves into something much bigger - hence this masterplan thingy (despite its being identified as about "capacity").