If the UK had a more equitable and democratic electoral system it (probably) wouldn't be in the mess it's in today.
Agreed, hence I'm a member of the Electoral Reform society, and long time whinger about FPTP.
So let's go back to some of your points, starting with this one...
The election should have been voided and re run IMO.
The election was run on the premise as it has been for decades. It didn't fall below any threshold for being valid and the popular vote issue simply is not relevant when it comes to the count. Should the system be changed, yes? Should we go around voiding the results of valid elections until then, no - absolutely not.
The UK also voted overwhelmingly against ditching FPTP in 2011. That may well have changed since voters who are used to being protected by FPTP are now falling victim to it, but for now, it's unlikely to be in the incumbents interest to move away from a system that got them elected, unless they were elected on that pledge, and although Starmer made noises about it - it's not really any closer to fruition.
But yes, the disparity between votes and seats is a problem.
Scotland, FWIW, voted to remain in the UK in 2014. They also voted to remain in the EU in 2015. Large scale support thereafter for the Scottish Nationalists would indicate that they wanted another go at both of those questions, but SNP support substantially dropped off prior to the last election.
Wales in this context is almost an irrelevance, their nationalist Party, Plaid Cymru, falls behind Labour and the Conservatives at their ballot box, and there's no meaningful talk of them wanting to leave the UK let alone having a referendum on it. Wales also voted to leave the EU, for some even more unfathomable reason, than the English. They don't want to leave the UK, and they didn't want to part of Europe.
Ireland, I'll leave well alone, it's a highly contentious topic and while I personally don't hold an opinion one way or another on it, whoever offers them the choice - even in the best of faith - may well end up with blood on their hands. Northern Ireland probably has the easiest route back to the EU, as Ireland is still a member, which probably does sway some peoples opinions over there on where their allegiance should be. As abstentionists Sinn Fein don't represent their supporters in Parliament, and the Unionist vote is split across multiple parties... I'd suggest any referenda held on this matter would be highly complex, but essentially there's no one that wants an independent Northern Ireland, they either want to be in the Union, or part of Ireland.
On the topic of EU membership. The EU won't negotiate with Scotland, Northern Ireland, or Wales on terms for their entry to the Union, because they don't know what state they'd be in after leaving the UK, and
they wouldn't know because at this time the Government won't negotiate with them on terms should another independence referendum take place. Nobody would really know what they were voting for prior to a referendum, which was a massive problem with Brexit, Ignorance easily beats caution.
With all that said, it seems you're into ignoring election results and breaking up unions against their will, no?