Disorder in the heterogeneous material stack of semiconductor spin qubit systems introduces noise that compromises quantum information processing, posing a challenge to coherently control large-scale quantum devices. Here we exploit low-disorder epitaxial, strained quantum wells in Ge/SiGe heterostructures grown on Ge wafers to comprehensively probe the noise properties of complex micrometre-scale devices, comprising quantum dots arranged in a two-dimensional array. We demonstrate an average low charge noise across different locations on the wafer, providing a benchmark for quantum confined holes. We then establish spin qubit control and extend our investigation from electrical to magnetic noise through spin echo measurements. Exploiting dynamical decoupling sequences, we quantify the power spectral density components arising from the hyperfine interaction with ⁷³Ge spinful isotopes and identify coherence modulations associated with the interaction with the ²⁹Si nuclear spin bath near the Ge quantum well, underscoring the need for full isotopic purification of the qubit host environment.