It's going to be better sound quality to come right out of the phono stage into the preamp. Otherwise you'll have the extra preamp circuitry and volume control in the signal path (a record or monitor out, as mentioned above, may bypass this circuitry). That said, if it's a big deal and you REALLY need the functionality and/or the extra gain of the preamp, it can be OK. I've tried it before (Rogue Hera II, Rogue RP-9, ARC Ref 6). I just always end up going back to the cleaner signal path.
If you need to convert SE outputs to XLR for a balanced headphone amp (some such headphone amps don't properly convert single-ended signals to balanced and will not sound their best), then Jensen makes some great ISO-Max transformers that will be more transparent than most preamps (even expensive ones). I've used these myself; they're great. You'll still need an extra set of interconnects, like with a preamp.
Do keep in mind that many headphones amps are built with one or two of the following in mind: 1. ability to support very sensitive IEMs, 2. expecting a really hot output digital source, especially on XLR inputs. This means that on many vinyl rigs, you will be running the headphone amp's volume control MUCH higher than you would for digital. This gets much worse if you choose low-sensitivity headphones; in fact it is possible to run out of volume travel.
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