The modded version also had some of those red caps on the backside. They probably replaced all the small ceramic decoupling caps. This may be the main cause of the added noise: the caps should be as close to the chips as possible. The longer leads just make it easier to pick up noise and add inductance.
A good observation, it was one of about half a dozen things I was hypothesizing might have lead to the increased noise, including the possibility of instability. This board wasn’t laid out with these unnecessary parts in mind. With digital hardware traces in proximity to the analog section, it may very well be pickup. In all-analog designs, stacked metalled film types are fine for both signal coupling and rail decoupling, though other precautions, such as additional series resistance for damping, may need inclusion.
That means
measuring, which is something these modders didn’t do. Modders are obsessed with capacitors.
In higher impedance circuits, these can be susceptible to EMI pickup. They’re not as bad as wound films, but care has to be taken. Electrolytics for coupling and SMD ceramics for decoupling would have been appropriate. They overlooked this.