Depends on what you are after, and what you want to do.
Integrated HDD will probably be a bit slicker and a bit less fluffing around to get connected and working - less to buy, less to connect, and no worried re: compatibility etc. Also, these units tend to be the higher priced more premium ones, and so typically (but not universally!) have better quality hardware etc.
Separate HDD is easier to move recordings around (say to a second identical unit in another where you want to watch them, or to transfer to a PC), and more upgradeable to a bigger disk or second one if you are running low on space and don't want to delete stuff yet. Also much easier to deal with if the HDD fails - which is one of the main failure points on HDD-based recorders.
flexibilty would seem to be a good objective. i was reading on another thread about the latest samsung recorder/player/smart box, that it is not easy to transfer recorded material to a computer.
so, altho the machine has amazing functionality on paper (twin freeview tuners, HDD, some internet capability) in practice there may be limitations
whereas if one had a separate twin tuner box with separate HDD and maybe a dedicated computer to access the internet, and all networked together, although setup would be trickier, in the end it could be a nice flexible system.
and as you say, individual components could (theoretically) be replaced/upgraded as necessary
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