I have only used splay shots in the context of paperless surveying, so do not have much variety of experience. The xvi produced from PocketTopo export > Therion import has always, for me, included splay shots, I think, regardless of various symbol-show, symbol-hide combinations I have used. So the problem is perhaps not that the shots are 'splay'. Try including; symbol-show group cave-centreline however, for the most part I think layout statements such as that affect only pdf and svg outputs... The symbol-show, symbol-hide combinations have given me reasonable control over display of splay shots in pdf outputs.
commenting out the splay flags to get the xvi right is not really a clean and sustainable option for large surveys.
If the data has been (is to be) entered manually then if you group all your splay shots together, say at the end of the survey data, I imagine you only need a single flags splay <all your splay shots here> flags not splay block of data. Then commenting out all the splay attributes is a single keystroke per survey. Could be a better workaround than using a text editor to do a find/replace? Bruce