Current 65-meera-new-fonts.conf contains:
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE fontconfig SYSTEM "urn:fontconfig:fonts.dtd">
<!-- SPDX-License-Identifier: MIT -->
<fontconfig>
        <!-- Generic alias this font to sans-serif -->
        <alias>
                <family>Meera New</family>
                <default>
                        <family>sans-serif</family>
                </default>
        </alias>

        <!-- For Malayalam sans-serif, prefer this font -->
        <match>
                <test name="lang" compare="contains">
                        <string>ml</string>
                </test>
                <test name="family">
                        <string>sans-serif</string>
                </test>
                <edit name="family" mode="prepend" binding="strong">
                        <string>Meera New</string>
                </edit>
        </match>
</fontconfig>

But it looks like upstream changed family name:
$ fc-query -f "%{family}\n" /usr/share/fonts/rit-meera-new-fonts/RIT-MeeraNew.otf
RIT Meera New

So even if rit-meera-new-fonts has a higher priority number in config more than google-noto-sans-malayalam(-vf)-fonts, the default fonts is being taken over by it when they are installed.

Reproducible: Always

Steps to Reproduce:
1.install both rit-meera-new-fonts and google-noto-sans-malalayam-vf-fonts
2.fc-match sans:lang=ml
3.
Actual Results:  
Noto Sans Malayalam will be picked up

Expected Results:  
RIT Meera New should be.

config file contains old family name of "Meera New". it should be replaced by "RIT Meera New".

I'm not sure when it happened. we may need a backport for stable releases perhaps.