Hi Ann and Fizz!
I'm from Dublin and live in the sunny south-east! I get JY to book me connecting flights from Belfast to link up with the main tour party in London. It's an extra 3 hours onto my journey, but I think it's worth it to ensure that if anything goes wrong JY will know about it and are obliged to sort it out (seeing as they booked the flights, not me!).
On my very first JY hol, I booked connecting flights from Dublin myself but it went disastrously wrong - first of all, the time of the UK departure was changed by Easyjet, so I had to rebook my Dublin flights and book overnight accomodation at short notice. On the way back, there was a lightning 24 hour national strike in Spain and Malaga airport was closed, so the whole tour party had to drive to Madrid and fly from there. The tour manager was brilliant and booked me new flights from Heathrow to Dublin (which she probably didn't have to do) but because I'd booked the original flight from the UK to Dublin rather than JY, I had to pay for the new flight which cost me an extra €260!
I know I was unlucky and possibly I could book my own flights from Dublin and all would be fine, but I prefer the inconvience of driving to Belfast (I have friends I can stay with overnight when needed, so I'm lucky that way) rather than missing my connection in London and ruining the holiday. If you book your own flights e.g. Dublin to Pisa and anything went wrong you'd be on your own - I'd prefer to have the safety net of the tour manager being on hand - and also a lot of bonding between the travellers happens at the airport, so you would miss out on that as well!
As far as I'm aware, JY can only book connecting flights that originate in the UK, which is why they can book me flights from Belfast but not Dublin. It adds extra travelling time onto my holiday and some extra expense, but as far as I'm concerned it is all worth it so I can enjoy the best holidays I've ever had!
I hope this is helpful, I know it's all a bit complicated and hard to follow but I hope you understand what I mean. If you have any other questions, I'd be happy to try to answer them.
Best wishes,
Bob