Hi there,
Thanks for the info; looks like a great build and fun project.
As for caps on the top plate; a question and some comments.
So, the question is what sort of a cap is it? A PS cap or something else? If it's a power supply cap, that's not unusual; a lot of tube amps have a 'Cap Farm' sitting near the Power XFMR and near the PS choke, sometimes betwixt the two (take a look at, say, a Dyna ST-70, vintage Marantz Amps, lots of SE amps - there are caps jutting out of the top plate right by - albeit an inch or two away from - the power XFMR). That it's such a common practice suggests to me it's not altogether bad though I don't know if a headphone amp sets a low enough noise threshold to make a difference. Breadboard it and see, perhaps?
The comments are that for some caps (say, the Jupiter wax/foil caps), if the power XFMR runs hot, the heat exposure might be a reason to relocate, as might the presence of high voltage on exposed wiring, depending on how well insulated or concealed from inadvertent contact it happens to be.