Since action economy is concurrent, I have an interesting issue.
I'm running a Bard 4/Sorc 3, and I have one 4th level spell slot. However my metamagic sorcery points only allow me to have up to 3 stored.
In order to maximize the effectiveness of my spell slot usage, when I'm at 0 sorcery points, I want to use the bonus action to burn the 4th level spell slot. This gives me 4 points back, however since I'm a Sorcerer level 3 I can't have 4 points banked.
So in order to not waste the 4th point when I burn that spell slot, I want to use it in the same turn by casting an Empowered spell. If I do this, and since actions are concurrent, I'll have used 1 point, and have 3 left over, which is fine because I can have up to 3 stored.
When answering, please consider that officially you can use a reaction during your action to counter a counter-spell with your own counter-spell and not interrupt your initial action. This demonstrates that the action economy is concurrent in 5e, removing any "stack" discussion from the equation.
Best Answer
The sorcery point limit always applies.
The scenario proposed in the question doesn't work; you never have an "extra" point to spend.
The rule for sorcery points is straightforward:
If you are a third-level sorcerer, and you have zero sorcery points, when you use a bonus action to convert a 4th-level spell to sorcery points, you have three sorcery points. 'Never' means never; the rule doesn't say "at the end of your turn" or anything like that; it simply says 'never'. You therefore can't "float" the extra point to simultaneously use for metamagic; in order to do that, you would need to have that sorcery point, and by the rule cited above, you can't have that point along with three other points.