Thank you for the additional information. I wanted to confirm what I was thinking.
First of all, without a medical exam, you can't be sure that he doesn't have an underlying medical problem, such as a urinary tract infection. Since his urine is a dark yellow, that usually indicates it is very concentrated. That may be normal for him, but can also be due to an infection. So, the first step is to make sure he is healthy and not urinating in the house because he's sick.
If there isn't a medical problem, then it would be a behavioral issue. In his case, it sounds like you've actually got 2 problems. The first is that his housetraining was never solid. He's learned that your bedroom is his den, so will avoid messing in there to the best of his ability, but he hasn't learned that the rest of the house is also part of his den. It probably doesn't help that Yorkies, like many small breeds, are notoriously hard to housetrain. I'll come back to the housetraining issue in a moment.
The second problem is hormones. At 9 months of age, small breed dogs are generally coming into adolescence. The urinating in the kitchen, especially when you are present and he could ask to go out, is most likely him "marking" his territory. This is a very common behavior
in intact males, of any breed, and can be hard to break them of it once they get in the habit. Since he is still young, and has just started the behavior, getting him neutered sooner rather than later should go a long way to stopping it.
The rest of stopping it would be in getting his housetraining completed. I would start by confining him to a smaller area than what he is being allowed in now. The bedroom at night should be fine, since he has already shown he can be trusted in there. (Though, to be honest, I don't leave any of my pups loose when I can't watch them, even overnight, until they are over a year old - not so much because of "accidents" but because of what they might chew on or get into and hurt themselves on.)
During the day, you can either try to confine him to your bedroom, or a small area where he can't do damage or get into trouble. Some possibilities would be a bathroom or a crate. Another would be to get an "exercise pen" and set that up in the kitchen, away from the kitchen chairs or anything else he can do damage to or urinate on. With the bathroom or exercise pen, you can set up an area where he is allowed to go to the bathroom - either on newspaper or puppy pads. If he can "hold it" all day while you are at work, then you can may not need the bathroom area, or can use a crate.
A brief comment on using a crate. Initially many dogs and puppies will whine and cry at being locked in. If you let them out while they cry, they learn they can whine to get out, and will only whine louder and longer next time. Much like a child throwing a temper tantrum to get his way. Once they get used to the crate, most view it as their den, and will often retreat to their crate to sleep or just get some quiet time. The trick is to not use the crate as punishment, but instead make it a good place to be - usually by feeding
them in the crate initially, and giving them special treats
or toys while they are in the crate.
Finally, when you are home, you need to make sure you can keep an eye
on him. If you are not actively watching him, you can try the umbilical cord method - keep a leash on him and have it tied to your belt. That way he can't wander off without you noticing. Make sure to take him out frequently, and praise and reward him for going to the bathroom outside. If he makes a mess inside, unless you catch him actually in the act, there is no point in punishing him. Even if you catch him in the act, the aim is not to punish so much as to interrupt him (usually a sharp or loud noise works), then take him outside where you can reward him for going where he is supposed to. Punishing him would be like punishing a toddler for using his diaper.
I hope this gives you the information you need. Please let me know if you have additional questions. Good luck with him.