Contrary to your assertion, you don’t use styles. The whole text is manually formatted. However this doesn’t change the problem (but for the fact mentioned in tdf#148257 that once CTL is enabled you can no longer force the language in the style).
I had to enable CTL, so perhaps you didn’t do it on your computer.
Digits: there are indeed specific Malayalam digits starting at U+0D66. It then depends on the input method utility in your Manjaro (not familiar with it, I use Fedora) whether ASCII digits on your keyboard are converted to Malayalam or not.
You can force them anyway in Writer by typing “U+0d66” (without the quotes) immediately followed by Alt+X for zero and other hexadecimal code up to U+0D6F MALAYALAM DIGIT NINE. They are followed by three glyphs for 10, 100 and 1000.
Punctuation: the Malayalam block does not contain specific glyphs for punctuation. You can perhaps “borrow” punctuation in other Brahmic sub-blocks. I found U+0970 DEVANAGARI ABBREVIATION SIGN which is said to be equivalent to full stop. But rules may prohibit to mix Devanâgarî with Malayalam.
Leading issue (line spacing): this is caused by the automatic choice of font in CTL context. The Font dialog allows to “split” the Unicode coverage into Western and CTL contexts. This is configured as Liberation Serif for Western and RIT Rachana for CTL. These fonts have not the same metrics and this causes the irregularity when characters from different blocks are mixed in a paragraph.
This can easily be fixed. Either you set CTL to Liberation Serif too because this font has a very wide coverage, or (because the shape of the glyph is not to your liking), you set Western to RIT Rachana as it is very likely that the font also covers a major part of Latin 1.
Then both languages will be set in the same font, clearing the metrics issue.
One last advice: learn to use styles. This will really ease your work. Read the Writer Guide.