If you create a customized preset, you can set Complexity as "Speed" mode to speed up the encoding. For the built-in preset like H264MultipleBitrate1080p, you can use PresetConfigurations.Complexity Property and set it as "Speed" to speed up the encoding. Please refer to the doc here:
https://learn.microsoft.com/en-us/dotnet/api/microsoft.azure.management.media.models.presetconfigurations.complexity?view=azure-dotnet#microsoft-azure-management-media-models-presetconfigurations-complexity
If you have further questions regarding the encoding performance, please share us more details about your source video: resolution, duration, and bitrate etc. A sample video will be better for us to test the performance for you. Thanks.