The bridge isn't the problem and never was. The track from St Brisbane to Bowen Hills is all just dual track with quad platforms at Roma St and Central only. Its triple track south of South Brisbane.
The congested part in Brisbane is from Park Road (junction of the Cleveland line) to Bowen Hills (junction of the Ferny Grove Line).
The tunnel provides an effective pair of tracks from just before (south) Park Road (Dutton Park) to just past (North) Bowen Hills.
I'm guessing the intent is to run all GC trains and most Beenleigh line trains via the tunnel.
Cleveland and some Beenleigh trains (I'm guessing the truncated starters from Kuraby) will cross the bridge which with the extra capacity will see about 14 to 16 trains per hour cross the bridge with a similar number in the tunnel. When the Greenbank line is built in the following 10 years, add another 8 trains an hour to fill most of the spare capacity.
The problem for the XPT is that it uses the DG track from the junction of the interstate at Salisbury to Sth Brisbane in the anti-peak direction. This track is used by the Gold Coast Express services heading north in morning peak. This distance is around 7-8km from Salisbury to the tunnel. The Triple track south of Sth Brisbane to Salibury is the worst designed triple track in Australia. The track is often way off to the side and makes it less friendly for south bound expresses, but ok for north bound. But trains cannot simply jump on or off as there is I think only a few options to do this.
Once the tunnel is complete, potentially hopefully there will be expansion of this track to 4 tracks between Dutton Park and Salisbury (start of the expanded triple track south to Kurby and built in such a way a 4th track is easy to add when the time is required, but unless 2 x are dual guage it will be limited value to the XPT.
As I said before, no Countrylink service runs in peak flow in Sydney and Brisbane has no Queensland Travel trains in peak either for the same reason so planning to put the XPT or its replacement back on the DG in peak is a pathway to certain failure.
Regarding long layover
Yes, the XPT fleet is insufficient for a long layover in Brisbane, however what is the fleet size for the XPT replacement?
Part of the current problem for NSW Trains is that its two incompatible fleets of trains servicing the Countrylink services is that it wastes time in Sydney. ie a Xplorer service may arrive back and could be turned around for next service, but the next service maybe an XPT service and VV. Hence is the govt procures a single platform to replace the entire fleet and does so in one go over say two years, there is likely to be greater timetable flexibility to deal with the issues of Brisbane without extra sets.
I've said it before and I'll say it again, the state needs a standard fleet made up of 3 and 4 car sets that can be joined to create 3, 4, 6, 7 and 8 car sets. Potentially the north coast services, made of two of these sets, could have 1 set be truncated in the lower part of the NCL, ie Kempsey, thus improving uterlisation and loading efficiency. Sim's has previously stated some "rumours" that there will be additional services in some areas, such as Wagga. If true this would support a larger fleet purchase. Additionally by avoiding through the night running the fleet can now be universal.
I'm not sure the XPT stops too often, many stops are as required and if there is someone there or someone to get off, so why avoid servicing your customer? Perhaps 1 or 2 stops could be merged but unlikely more than that. The 14hr trip is not because of the a dozen stations, its the track. I could be wrong but I don't see the inter-capital trains as competing with inter-capital traffic, rather more local and to/from the big smoke.