If you're shooting raw then HLTP and ALO (Auto Lighting Optimiser) should both be disabled as they can significantly increase noise in RAW images.
There's been some debate about this, and the conclusion, which seems right, is that Highlight Tone Priority impacts the Raw and is embedded (hence the restriction on lowest ISO) but Auto Lighting Optimiser is a post-capture application and only affects the JPEG.
HLTP does increase noise, because it effectively puts an extra stop of ISO gain in the shadow end, in order to hold those extra highlights. I guess that,
if this is the effect you want (extended dynamic range, which generally I find I do) it's moot whether it's better to apply it in-camera directly to the Raw, or afterwards in post processing, eg with the Fill Light slider in Lightroom.
I suspect that there's nothing much in it, but in theory doing it in-camera should be better? I've not done any comparison tests myself. But if you decide you don't want the effect after all, you're stuck with a bit more shadow noise...
On the other hand, if you shoot with HLTP and drop the ISO a stop from your normal setting, you should retain the extra highlight detail and the extra shadow noise should be neutralised?