The bot currently uses {{ढाँचा:नमस्ते|realName=|name=insert name here}}, but for the current version of the welcome template to work it needs to be like {{subst:नमस्ते|realName=|name=insert name here}}. Rather than transcluding the template, it should be substituted. Thanks.
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If I understand the extension documentation correctly, this can be done by creating https://ne.wikipedia.org/wiki/%E0%A4%AE%E0%A5%80%E0%A4%A1%E0%A4%BF%E0%A4%AF%E0%A4%BE%E0%A4%B5%E0%A4%BF%E0%A4%95%E0%A4%BF:Newusermessage-substitute, which any administrator should be able to do.
MediaWiki:Newusermessage-substitute is created but the bot doesn't seem to be working anymore.
This sounds like a good support question for https://meta.wikimedia.org/wiki/Tech and does not sound like a server-side configuration or software code issue?
I am closing this task as I don't see any issue. It is working fine. See विशेष:Contributions/नेपाली विकिपिडिया स्वागत. @Badakaji Please consult the community first, if you have any confusion. Thank you for your understanding.