I'm unconvinced about the 'Updated Seals' argument. MY07 still has many original seals but did have warranty 'remedial work' done . Seal leaks are caused by assembly problems, the design which hasn't changed much, and/or lack of seal care maintenance by owners. When the EOS was first sold, dealers were telling buyers that only routine maintenance was required when in fact there was a specific V.W procedure for roof seal maintenance, but at extra cost.
Who has replaced a 2007 top of roof important seal with an 'updated part' - show us the evidence of changes? If you look at the maintenance operations for replacing EOS seals, there are some pretty tricky things to do which would have been part of the assembly process. The average garage workshop would not be familiar with this kind of work.
Whether an EOS roof leaks or not (They probably all do to a small extent) depends on how much care has been taken with roof seal maintenance and spotting any leaks before they get worse. All EOS's whatever their year require regular preventative roof maintenance.
MY07 is the TDi Sport. Timing belt? - No issues whatsover when replaced according to V.W recommends. The main issue for looking at a later model would be the level of spec. because this affects many 'options' which you can expect as standard in a new Asian brand vehicle. My TDi Sport is Lowline spec. which means basic features like cruise were missing. Some features can be added retrospectively, but from about 2009 their electronics were more versatile and had more potential for making these changes.
IMHO Apart from the above, if somebody offered me a low mileage 2007 that was dry and had had roof service and leak checks done twice a year and a 2009 that had had nothing done (Sir, later EOS's had better seals and don't leak!) I would take the 2007 and pay less money.
If you want to buy an EOS of any year, assume they can all leak , particularly parked outside 24/7. Avoid the worst and give roof seal TLC to the others from day 1. That's the problem with desktop research and buying off the page. Too many assumptions can be made and it's only by carefully looking at a car in realtime can you reduce the risk of buying a lemon. Don't buy an EOS unless you are prepared to put in more time yourself or pay others to keep it well maintained and leak free. If you want a reliable 'jump in and go' regular regular commute car, there are plenty of non-cabriolets alternatives to choose from.
Perhaps we should start a survey listing EOS years by number of leaks? I bet most will get leaks of some sort once they are over 3 years old. All the other cabriolet brands can have similar issues, but an EOS is probably cheaper to put right than a Merc.?