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For universal quantum computation, a major challenge to overcome for practical implementation is the large amount of resources required for fault-tolerant quantum information processing. An important aspect is implementing arbitrary unitary operators built from logical gates within the quantum error correction code. A synthesis algorithm can be used to approximate any unitary gate up to arbitrary precision by assembling sequences of logical gates chosen from a small set of universal gates that are fault-tolerantly performable while encoded in a quantum error-correction code. However, current procedures do not yet support individual assignment of base gate costs and many do not support extended sets of universal base gates. We analysed cost-optimal sequences using an exhaustive search based on Dijkstra's pathfinding algorithm for the canonical Clifford+$T$ set of base gates and compared them to when additionally including $Z$-rotations from higher orders of the Clifford hierarchy. Two approaches of assigning base gate costs were used. First, costs were reduced to $T$-counts by recursively applying a $Z$-rotation catalyst circuit. Second, costs were assigned as the average numbers of raw (i.e. physical level) magic states required to directly distil and implement the gates fault-tolerantly. We found that the average sequence cost decreases by up to $54\pm 3\%$ when using the $Z$-rotation catalyst circuit approach and by up to $33\pm 2 \%$ when using the magic state distillation approach. In addition, we investigated observed limitations of certain assignments of base gate costs by developing an analytic model to estimate the proportion of sets of $Z$-rotation gates from higher orders of the Clifford hierarchy that are found within sequences approximating random target gates.