Thanks all for the re-assurance. I've already completed the schematic a few days ago at least I can now be confident in proceeding with pcbnew.
One thing to keep in mind is that Vincent was likely not comparing the output to other hobbyist tools like Eagle, but to a professional tool like Altium. So don't automatically assume that Eagle will fix whatever flaws Kicad might have.
That's a good point, I mention eagle because I have had no major problems getting PCBs made using it. (granted they were nothing too complicated, just a few vanilla boards.)
The gerber format is fairly standard and is the linchpin of my communication with the pcb fabricator. Therefore whether using altium, eagle, kicad (or protel 99/se & Proteus back when this was my job) the gerber output should be reliable and the same across the board (pun intended). edit: I am aware that all tools have their own unique set of quirks and bugs that either get fixed or I can live with, and if I can't then I use an alternative.
I'm pleased that whatever the issues were, they were dealt with.
After starting this thread i started to look deeper into the proposed future developments and contributors to kicad, if they are implemented correctly kicad will reach maturity fairly soon, and the quirks will be replaced by new ones.
I look forward to it.