Ꜣ and ꜥ

The Unicode standard makes provision for separate characters for capital and small Egyptological aleph and ayin. This is at odds with modern practice, not least because non-Unicode fonts do not distinguish between these characters. Hence, D. A. Werning earlier suggested using capital aleph and ayin in all positions, as capital aleph and ayin look better in most modern fonts. This practice is followed in the Rubensohn-Bibliothek. However, in earlier Egyptological publications and most notably in A. H. Gardiner’s Egyptian Grammar, capital and small forms are distinguished from one another, as pointed out by W. Schenkel. Besides, distinguishing between lower- and upper-case characters is deemed semantically more correct than always using capital letters. Hence, the Ramses Project and Totenbucharchiv use small aleph and ayin. Werning adopts this practice in the modern version (2021) of his convention.

ꞽ

The encoding of the Egyptological yod in Unicode remains an unsettled issue. Generally, one of the three combining signs U+0313, U+0357, or U+0486 can be used to transform an i into yod.
In 2017, D. A. Werning recommended the use of the dotless ı (U+0131) in combination with U+0357, and this recommendation was adopted in the Berlin Text System (BTS) of the Thesaurus Linguae Aegyptiae and was recommended on the EpiDoc page. However, the official Unicode FAQ then recommended using the ordinary i (U+0069) as base for any of the three combining diacritic characters.
The ordinary i is used in combination with U+0357 in the Totenbucharchiv and is recommended by D. Mastronarde. Werning advocated this approach in the 2018 version of his recommendations.
Another widely accepted approach is the use of the ordinary i in combination with U+0486. This combination was used in the keyboard layouts by S. Rosmorduc and recommended by Brill Publishers.

Unicode 12.0 (March 2019) defines new characters for Egyptological Yod: ꞽ = U+A7BD (Latin small letter glottal I) and Ꞽ = U+A7BC (Latin capital letter glottal I). This should become the new standard. As of February 2022, these characters are supported by a number of freely available fonts, including Andika, Andika Compact, Charis, Doulos, and Gentium Plus by SIL, New Athena Unicode and recent versions of Noto Serif. The Brill Typeset 4.0 also supports these and other transliteration characters; however, it only free for non-commercial use. Full support is also provided by Calibri 6.26 and Tahoma 7.01, supplied with Microsoft Windows 11 and Microsoft Office. See a comparison of these fonts.
The use of U+A7BD and U+A7BC is the current recommendation by D. A. Werning.
Unlike the capital and small variants of aleph and ayin, different encodings of yod are despite similar outlook mutually incompatible; as per the official Unicode FAQ, computer software considers them completely different signs, not variants of the same sign.

i̯

i̯ (i and U+032F) is used in the Berlin Text System (BTS) to encode weak last consonants in verbs. It corresponds to i in the non-Unicode online version of the Thesaurus Linguae Aegyptiae. With this option selected, the Converter also makes other transformations to make the transliteration compatible with the BTS.