The mark may be placed in any of the four corners of the Chinese character. In modern Mandarin Chinese the locations map to tones as follows:

lower left: 1st or 2nd tone
upper left: 3rd tone (some cases 4th tone)
upper right: 4th tone
lower right: not applicable for modern Mandarin

Examples from the text:

重 zhòng (adj) heavy, important
꜀⁠重 chóng (adv) repeatedly; (measure) layer, storey

語 yǔ (n) spoken language
語⁠⁠꜄ yù (v) to tell, inform

For more details on tone marks, look up articles on ‘Middle Chinese tones’ or see:

Williams, S. Wells. 1874. A Syllabic Dictionary of the Chinese Language; arranged according to the Wu-fang Yuen yin, with the pronunciation of the characters as heard in Peking, Canton, Amay and Shanghai. Shanghai: American Presbyterian Mission Press.
Introduction SECT. IV.—SHING OR TONES.

Transcriber’s Note: Cover.

The text on the cover is “大寶廣博樓閣善住祕密陀羅尼” or “The Great Increasing Jewel, Fathomless Celestial Mansion, Extremely Well Abiding, Secret Holy Mantra” and “法顯傳” “The Story of Faxian”.