Note that it's an open question if the Scots economy would remain worse per capita, not disagreeing there is/was pain ahead in transition.
The best thing is that Slovaks had to stand on their own feet and their nationalists slowly had stop blaming everything on Prague. This kind of whiny nationalism embodied by then-prime minister of Slovakia Vladimir Meciar is somewhat disgusting and I can see its softer version in Scotland right now.
The worst thing is that yes, our international weight has gone down significantly.
But there was customs union between CZ and SK even after the split. I cannot imagine the economic pain if the former federation was suddenly divided by a hard border, as Scotland and England would be.
It doesn't have to be, even if Scotland was part of EU and not England.
UK and Spain/EU negociated maintaining some of the Schengen rules for the Gibraltar/Spain border despite its status still being disputed by Spain and a bumpy history. There is no reason Scotland and rest of UK cannot have a treaty allowing soft border.
"Remain" is doing a lot of work here. Scotland runs a sizeable deficit with the rest of the union and with the decline of North Sea oil revenues that will only increase. Of course that might not "remain", but leaving the UK and then joining the EU is going to create a 5-10 year period of turbulence as well.
Still, there's more important things than GDP.
Smaller vs larger has arguments on either side. I think when you’re talking about major world powers there’s an appeal to not downsizing.