If it's restricted stock, either the grant is taxable income, or the stock is paid for at the time of the grant (write a check to the company). Vesting is then defined a reducing percentage of shares the company can buy back over time, and so if the employee leaves or vesting terminates for some reason, the company writes a check to cover the refund.
This all works best in the early days when the 409a valuation is zero. Once you have a high valuation, getting real amounts of equity into employee hands that has a good chance of actually being valuable in the future is extremely difficult, because with each share you give to an employee you are giving essentially 40-50% of that to Fed + State, plus another 30% of any future gain. Since this is all based on fantasy valuations of an illiquid asset, it is playing with fire in the worst way.
The only other option is options with high exercise prices based on highly speculative earnings forecasts, for shares which are 2nd or 3rd in line behind all the preferred stockholders. This might work out for late hires at Google and Facebook, but almost never anywhere else.
I mean think about it -- "Here are some common shares of my company; I just raised $50m at a $500m valuation, we are burning $5 - $10m in cash every quarter. We are are going to be absolutely massively huge and a billion dollar unicorn in no time. There are currently $100m of preferences ahead of you, and we will certainly need to raise huge amounts of more cash in the years ahead to achieve our vision. You will have no input into how the company is run, no effective voting power, and no seat at the table during an acquisition. Our 409a valuation is just $100m!" As an employee, getting an option to pay for that is supposed to be an incentive?!
The solution I would like to see? Illiquid shares in a private startup less than 5 years old and with assets less than $100mm should be valued at a discount to liquidation value, or ideally transferable with no taxable event whatsoever. If those shares are encumbered or sold, then the holder pays short or long-term capital gain rates on the full amount of the sale. No 409a, no exercise price, no 83(b). There's absolutely no reason to try to pre-tax a portion of the value of the shares up-front when they are illiquid and impossible to value. This proposal is basically tax-neutral. If you want, you could extend the short-term capital gains rate to 2 or even 3 years instead of 1 for this type of transaction, to avoid someone taking highly valuable shares of a later-stage company, and getting the full amount taxed as capital gains just 12 months later.
To put this in perspective, with QSBS / Section 1202 (qualified small business stock) the first 10x or $10m of gains on original issue shares is 100% Federal capital gains free after a 5-year holding period. This was made permanent in 2015. Some states also eliminate or reduce the state capital gains as well -- although not California for a few years now :-( So politicians are making startup investing very attractive for anyone who can get Founder/Restricted or Preferred shares, but they have left the employees' options completely in the dark ages. It's time to fight for some reforms here...