Please add
<assign|sectional-normal|<macro|name|<wide-normal|<arg|name><no-page-break>>>>
<assign|sectional-centered|<macro|name|<wide-centered|<arg|name><no-page-break>>>>
to the preamble and you will have the paragraphs below section. For the equations:
<assign|equation*|<macro|body|<\with|mode|math|math-display|true|par-ver-sep|<eqn-ver-sep>>
<surround|<no-page-break*><vspace*|<eqn-short-above>><no-indent><htab|0fn>|<htab|0fn><vspace|<eqn-short-below>>|<arg|body>>
</with>>>
and as far as I understand one needs to redefine every environment after which there is no indent by default while he wants to have indents, because it is not possible to redefine the <no-indent*>
macro (“don’t indent after”), which is used in these environments to prescribe the absence of an indent, that is it is not possible to redefine <no-indent*>
e.g. to do nothing.
Please let me know if now it works for you (keeping in mind that you might have to redefine some other environments).