The discoloration is from leakage of blood the the microscopic vessels called capillaries. It happens when the pressure you are making (from outside in, in the case of pumping) forces the capillaries to leak. That can come from pumping, squeezing, Ulis or clamping (the last three are from increased pressure from within). The reason it is probably happening at a certain part of your shaft is that the base of your shaft is likely either touching the sides of the tube, or your wrap or seal on the tube is in the normally colored region. It happens this way because the pressure from the tube or seal on the tube acts as a counter pressure to the expansion pressure pulling the blood out of the capillaries.
Your capillaries are likely getting traumatized, but unless the bruises are continuing to darken or enlarge after you are done with your session then they aren’t damaged, per se. In either case, they are very superficial and only serve the skin in that region, and are innumerably redundant so even if you damage a few per hundred you will see your skin darken without risk to the skin tissue perfusion.
It is possible for the darkening to be somewhat permanent, but it is unlikely. Typically (and especially around here) “permanent” can mean a few weeks or months. If you stop for a few months or in some cases a year or so, it will likely fade back to normal.
The things to do to prevent it: use less pressure, longer duration. Do not take any blood thinners (including aspirin, alleve, or ibuprofen), jelq in the shower for a bit to improve clearance of the blood products deposited in the skin, and don’t worry about it too much. If you have a date or a photo shoot or something (whatever is driving your urgency here) you might consider stopping a few days out, following the advice around here for clearing it up and then only pump light pressure for long duration the day you want to maximize your temporary size.
You can also try to even out he discoloration to go along your entire shaft (or as much as possible) so it doesn’t look like Neopolitan ice cream. Try changing the circumference of your pump so more of your shaft is getting expanded. Try clamping/ Uli’s at the base for the same effect. If your whole cock is dark, it might just look like you have a dark cock.
Lastly, if it is sex that is driving your timing issue, you can put on a cock ring during, which will also darken your cock while it is on. If the partner asks about it, you can say you like to use it and not to worry about the color. Tell them it makes your dick a little fuller and feels great for you during sex and masturbation. Better for them, too, because of the extra added girth and hardness. Sometimes there is some temporary discoloration for a bit after you take it off, but it usually goes away in a couple of days if you don’t use it. I have used this approach with multiple partners, including long term girlfriends and my wife, to keep the PE stealth but explain the occasional weird color it brings. None of them have ever thought twice about it after that.
Hope this helps.