Looking to get a full same colour respray for the coupe and have two options.... windows in/out.

Price wise it’s about £500 more for the latter option.

Beyond a tidier finish does it really make that much difference? My view is that the paint will be cut in and so long as it’s masked up correctly would/does it make it very obvious that it’s been painted? Any issues with longevity?

Anyone with experience able to comment?

Windows out is always a better option as long as its a competent bodyshop.
The window rubbers/surrounds often get treated with silicone products that paint won't stick to, which is much harder to remove with the windows still in place.
Downside of removing the glass is it needs to be done carefully and refitted properly to avoid leaks.

500 STERLING to remove windows,ouch thats a very high price,guys in AUTOGLASS here in ireland quoted me 240 euro
And yes if your doing a full respray i would advice removing all glass,windows,i would not let the bodyshop take out the glass,but get a proper window removal company to remove glass for the bodyshop,then get them to fit it back in properly.
If your going to trouble of respraying and paying for a proper re-paint why take the chance off a bodyshop not masking,sanding around windows,for it to start peeling off after about a year,also one main areas for vintage cars to start rusting is around window frame edges,under rubbers that we cant see,so you would be paying again in a year or so because off rust under rear quarter panel window frames and rust under front window under where the wiper fiberglass panel is located.
I HAVE 32 years experience restoring cars in a bodyshop,and always advice customers to remove all glass for vintage,classic cars been fully resprayed.
At moment fully rebuilding restoring a 1999 coupe 20v turbo LE,also dismantling a 20v non turbo,and 20v turbo,all seem to have rust problems in same area,under front wheel arches,inside boot floor,inside and under rear quarter panels,make sure you take out rear interior to check inside rear quarter panels,also all had problems where front wiper moter panel is under the fiberglass covers.
Hope this helps robert.