I don't think what you said would count against you, but I think you could do better. If I read that, it wouldn't count against you but it also wouldn't count any more positively than if I received no response at all.
Your response is quantitative and objective. Because of that, it's kind of like you aren't thanking the person for their role/decision, but instead just thanking an entity (company) for optimizing to a new fact (value of professional progress) in a way that you knew it should. To cut to the chase, that translates to you de-emphasizing their individual role, not acknowledging their discretion and autonomy in the matter and conveys a sense of arrogance that you know what they should do and they finally caught up to you on that.
The whole point of the communication is to convey that you are happy that somebody did something. Therefore, you want to emphasize the people (i.e. "you" vs "the company"). You want to emphasize their role ("that you decided" vs "that the company values"). You also want to emphasize the fact that they could have not done this. When you say "I'm glad" it kind of sounds like it was just meant to happen anyways so it has that undertone of arrogance. The more inevitable and obvious you make it sound, the more it diminishes their action that you are appreciating them for. Appreciation is a lot more meaningful when it's not for compliance with the laws of the universe, but instead for more voluntary aspects. Consider the difference between somebody saying, "I appreciate that you gave me some of your food" and "I appreciate that you landed back on the earth after jumping". ... the more involuntary, the less meaningful the thank you.
Also, I don't think it's a matter of being "junior". In fact, I'd say being overly formal in internal operations is more likely with a new hire who is a bit nervous about how they will be perceived. Where I work, whether somebody is an executive or an assistant and whether they are a new hire or a long time employee, I'd expect a lighter and more friendly kind of thank you simply because humans in general tend to be friendly and subjective. There are some objective and perhaps cold people (probably including me, I'm a computer type too, so most of my communications involve making things objective and defined), but overall most people here, even those who are extremely dedicated and productive, are friendly, personable and balance subjective and objective. Over-reliance on a cold objective stance may be good in writing software specs, but the fact is, every company comes down to people. Making people feel good, making people feel appreciated, making people happy and developing bonds with people is central to making an effective company/team. While you don't have to be going out to the bar with your coworkers, being kind and friendly, rather than simply "down to business" is in the best interest of both the company and the workers. Being professional is absolutely, definitely not at odds with being outgoing, kind, friendly and even joking around a little bit. These are all tools to help communication and interaction be more effective and communication is a central to basically any job. Most of the top executives where I am are completely professional, but will still joke around a little bit and certainly say things like "thank you". When I do a good job, the people at the top of the company certainly say things like "Thank you!", "This is going to make things so much easier!" and "I don't know what we'd do without you" rather than just "We appreciate your completion of X." I work at a big place too; this isn't some sort of small, loose start-up. This is a massive, bureaucracy with rules, committees and regulations for everything.