Vision tool-use reinforcement learning (RL) can equip vision language models with visual operators such as crop-and-zoom and achieves strong performance gains, yet it remains unclear whether these gains are driven by improvements in tool use or evolving intrinsic capabilities. We introduce MED (Measure--Explain--Diagnose), a coarse-to-fine framework that disentangles intrinsic capability changes from tool-induced effects, decomposes the tool-induced performance difference into gain and harm terms, and probes the mechanisms driving their evolution. Across checkpoint-level analyses in the crop-and-zoom setting on two VLMs with different tool priors and six benchmarks, we find that improvements are dominated by intrinsic learning, while tool-use RL mainly reduces tool-induced harm (e.g., fewer call-induced errors and weaker tool schema interference) and yields limited progress in tool-based correction of intrinsic failures. Overall, in the crop-and-zoom setting studied here, current vision tool-use RL learns to coexist safely with tools rather than master them.