Both devices can change voltage, but they do not provide the same protection boundary. Choosing between a transformer, an autotransformer and a converter starts with whether galvanic isolation is required.
Start with the isolation requirement
An isolation transformer has separate input and output windings. An autotransformer shares part of its winding between input and output and should not be assumed to provide the same isolation.
Review the complete equipment architecture: accessible conductive parts, protective earth, external signal connections and the destination installation standard all influence the decision.
Compare size, loss and range
For modest voltage ratios, an autotransformer can be smaller and more efficient because only the transformed portion of power passes through the common winding.
Do not compare apparent compactness alone. Enclosure, protection, tapping range, cooling and the cost of adding isolation elsewhere can change the system result.
Control the operating and fault conditions
Define input and output voltage ranges, tap arrangement, load current and any unbalanced or transient conditions. For three-phase equipment, state the phase and neutral configuration.
Plan protection against overvoltage, short circuit, mis-selection and accidental contact. Label the equipment so users do not confuse a voltage converter with an isolating supply.