Have you tried using tsMuxeR? If the files are Blu-ray compliant, just let tsMuxeR multiplex them into either Blu-ray or AVCHD. It accepts SRT subtitles, but does convert them to PGS.
I have always used the default settings for subtitles with multiAVCHD, and do not use it to reencode or change subtitle fonts size and type. Just use it to author compliant files.
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