Hi AJ. With no experience of wood burning, except the rare firing of log stoves when in holiday homes.... but I can imagine the problem...
Wood - naturally - varies widely, as does its derivative, coal. Considering it is simply a lump of mixed hydrocarbons... all of mixed complexity, almost every chip is different from the next.
But my simple understanding of hydrocarbon combustion is as below:
The heat of the existing fire - and firebox - in 2 forms (conduction of adjacent hot or burning gases and radiant heat from further away, but which can penetrate some depth into the lump of wood) simply causes the lighter hydrocarbons to flash-off quickly, and without adequate air and turbulence will just form a rich combustion mixture. This makes CO and unburned hydrocarbons. Just like in a petrol engine that is rich. The CO is fuel that needs oxygen from the air, and a temperature over 350C so that it burns. Otherwise it is clear gas that is wasted fuel (half of the carbon is "unburnt"). The hydrocarbons, due to heat and the random way they are formed from having most of the hydrogen stripped off, then recombine into heavier hydrocarbons that need a much higher temperature and oxygen from air to burn. This is the black smoke that is a lot of unburnt fuel. Yes there is also free carbon in that mix of unburnt hydocarbons, but also other HC compounds like waxes, heavier oils, etc. It is the problem of the "oil refiner" to manage the re-engineering of mixed hydrocarbons (crude oils, etc.) into their various fractions that are created by "cracking the crude", I.E. separated, at different temperatures and pressures, then re-combined as appropriate to make other things like plastics, oils, etc.. The wood or coal fire in your boiler is just like uncontrolled cracking! But inside the fire, there are zones where all the hydocarbons molecules have been stripped away and pure carbon is left. This charcoal burns really well as it is in the air-rich lower levels of the fire, where air is drawn-in through the bottom bars. The temperature is over 800 C and glowing red as the carbon burns with air to CO and CO2. It also gives off lots of radiant heat that heats fuel above and walls of the firebox (thus making steam), as well as hot exhaust gas.
So a closed throttle reducing the draught, stops a lot of air being drawn through a fire, that is at conditions for combustion for the wider throttle combustion air draught. Thus a rich mixture is formed and causes the black smoke. Closing the throttle progressively allows the fire temperature profile to adjust and less black smoke is formed.
When new fuel is added, it is rapidly heated from the fire beneath and lots of light hydrocarbons are emitted, thus making the gas above the fire very rich (also with depleted oxygen from air passing through the fire) necessitating opening the fire door to allow extra top air to burn these hydrocarbons. But cooling of exhaust gases from the fire beneath, by both the cold new fuel and extra cold top air, can prevent complete combustion of these hydrocarbons, so making it difficult to avoid black smoke, especially with very "wet" or oily fuels. Hence drier "steam" coal is best to avoid this, or harder woods, of less oily varieties. Making holes in the fire allows extra air in, that is preheated by the fire, which helps to keep the above-fire temperature up, and helps this combustion to happen before the flue-tubes. Thus reducing black smoke.
If your boiler using wood pellets is a commercial device, I would expect it to have temperature sensors and even O2 sensors to feed an automatic controller to avoid over-fuelling and black smoke. But if a simple burner, then you have to imagine the temperatures and control fuelling and air factors yourself.
Hope this is of some use,