AFAICT, there is no bug here. It's just confusing how Unicode right-to-left characters in the repr() can modify how it's displayed in the console/terminal. Use the ascii() representation to avoid the problem.

> The same behavior does not occur when directly using the unicode point
> ```
> >>> s='000\U00010900'

The original string has the Phoenician right-to-left character at index 1, not at index 3. The "0" number characters in the original have weak directionality when displayed. You can see the reversal with a numeric sequence that's separated by spaces. For example:

s = '123\U00010900456'
>>> print(*s, sep='\n')
1
2
3
𐤀
4
5
6
>>> print(*s)
1 2 3 𐤀 4 5 6

Latin letters have left-to-right directionality. For example:

>>> s = '123\U00010900abc'
>>> print(*s)
1 2 3 𐤀 a b c

You can check the bidirectional property [1] using the unicodedata module:

>>> import unicodedata as ud
>>> ud.bidirectional('\U00010900')
'R'
>>> ud.bidirectional('0')
'EN'
>>> ud.bidirectional('a')
'L'

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[1] https://en.wikipedia.org/wiki/Unicode_character_property#Bidirectional_writing