How much did it 'cost' slave-owning nations to emancipate the slaves as a percentage of GDP?
Unfortunately, I'm not sure this will really answer the questions you raised to your satisfaction, but I can at least give some of them a try:

First Note: It wasn't 40% of the GDP of the Empire, but rather the 20 million GBP sum was equivalent to 40% of their annual governmental expenditures (or 5% of the Empire's contemporary GDP) source here.

Regarding your first couple of questions: unfortunately, there's no good, useful answer that I can find. If you were interested in calculating these numbers yourself, it might be worthwhile to look at this online database of payments made under the act. That said, it's important to remember that, as colonies of the British Empire, there might well be many reasons that could make the desired "contemporary GDP amount" difficult to calculate. For example, if there's an individual who owned plantations in Trinidad and the Bahamas, they themselves might live in London. Thus, for all practical matters, the compensation payment the plantation owner would receive doesn't flow to either colony, and shouldn't be considered in those colonies GDPs.

As for "how did they come up with 20 million GBPs?" While I haven't seen a specific answer, I'd imagine much the same way compensation pools are created today- by Parliamentary negotiation, estimation and extrapolation. The number itself is known exactly (that is, we know it's 20 million, and that's not an estimation on the part of the Guardian) since it's inscribed in paragraph XXIV of the act itself (have to scroll down a bit, or search on the page for "million"). That said, there's specific information in paragraph XLV of that act how the sum of 20 million GBP should be divvied up between the different colonies, and that's based on the local "value" of slaves in each colony for the previous eight years.

About additional compensation- no. Remember, there weren't really those "national governments" at the time. They all were, by definition of the act, only territories which were still completely ruled by the British crown. As far as I know, no regional governors supplemented that pool (I'm not even sure if they would have been allowed to, since the authorization for the payments in this case were from the British Parliament, and the vehicle to disperse the payments was a commission set up by the act).

Finally, I'm not exactly sure what you mean by "how would you cost the six years of unpaid labor." Who are you referring to "costing" this? The value of this labor wasn't included in the payments by Parliament. If you were thinking about what the effective cost of this provision was (that is, how much it cost the slaves whose freedom was delayed by those six years) then again, I think it might be an open question.

Again, I'll check back later to see if I can help by refining my answer. Let me know how this aligns with what you were looking for. Also, these additional resources might provide a bit of useful info!
NB: the total number of slaves freed uner this act is roughly 800,000