May or not track reliably due to limited sky view, multi-path reflections off the balcony confusing the receiver, and possible anti-glare or anti-heat reflective film on the glass.
I'd suggest taking a flat USB extension cable, that could be fed out through the patio door and the door seal closed on it to get the receiver right out to the edge of the balcony, and possibly even magneted to the hull exterior, some bluetack (to guarantee a water seal round the cable), and a roll of silicone self-amalgamating tape, to seal the GPS puck USB plug to extension cable joint.
Also take a hand-held GPS receiver that runs on AA batteries you can strap to the balcony rail as a backup + enough batteries for the cruise duration + whatever software you need to download and merge tracklogs from it and export to your mapping software.
You also need to consider non-destructive cable management and fixing. Gaffer tape and goo-gone may help!