I have started using Monaco
as my coding font. I also use this font in Konsole, KDE Terminal emulator. I don’t know since when, but iy has been a while that font in Konsole appears mis-aligned. Monaco is a fixed width font, so this problem is somewhat weird.
As usual, a google search took me to this
post and made these lines at the end of my ~/.fonts.conf, before
<test name="family" compare="eq" qual="any"><string>Monaco</string></test>
<edit name="autohint" mode="assign"><bool>false</bool></edit>
<edit name="hintstyle" mode="assign"><const>hintnone</const></edit>
And this has really solved my problem for now.