You'll have no issues with customs/immigration.
A year or two ago, I arrived on QF29 Saturday morning and departed on QF128 that evening.
I'd already done the peak, peak tram, 15 bus down from peak, star ferry, escalator, walk up nathan road, "Ladies" market, "Stanley" etc. SO I did some stuff I had not done before.
I went to the Plaza Premium Arrivals lounge for a shower (exe but comfortable)
Hong Kong .
Topped up Octopus and stored luggage.
Number E21 bus to Tung Chung then Ngong Ping 360 to the rather large Buddha. Walked up to it, in it, around it then back down through 360 'village' for a few of the sights/exhibitions. Back to Airport via 360 and E21.
Airport Express to Central then tram to North Point and started back. It was a tough trip after an hour or so on Tram, so jumped off at Tin Hua and took MTR back to central then AE back to Airport; by this time it was around 4pm. Collected bag and checked in. Hit the Wing, went to Pier, walked back to QF Flounge and a little later boarded QF128.