1. Summary
Use RunKit theme maker.
It not documented for June 2019.
2. Demonstration
Gutter line numbers in left side has a bad visible.

I edit Text
parameter in theme-maker.


(But besides line numbers RunKit also change text color of my notebook.)
3. Disclaimer
Data of this answer were relevant in June 2019 and may be obsolete in the future.
Method of this answer is uncomfortable, and I very hope that in the future there will be another.
4. Note
You can't overwrite embed RunKit and any another iframe styles of another domain via CSS:
5. Sources
5.1. Without styles
I attach RunKit to existing element.
<script src="https://embed.runkit.com" data-element-id="KiraRunkit"></script>
<article>
<pre id="KiraRunkit">
var stringSimilarity = require('string-similarity')
var similarity = stringSimilarity.compareTwoStrings('Кира', 'Кирк');
</pre>
</article>
body
height 100%
overflow hidden
background-color sienna
article
margin-left 2rem
margin-right 2rem
// [INFO] Responsive iframe:
// https://medium.com/@mahbub_hemel/how-to-make-your-video-iframe-responsive-a8c5fda821ba
#KiraRunkit
width 100%
position relative
iframe
width 100%
height 100%
position absolute
/* [INFO] Instead of frameborder — http://stackoverflow.com/a/10831379/5951529 */
border 0
5.2. With styles
I programmaticaly create a notebook. Options:
element
— HTML element, for which you will apply RunKit.
source
— full source of your RunKit notebook; use \n
for line breaking.
syntaxTheme
— theme, that you create.
JavaScript code you find in your theme-maker page.
<script src="https://embed.runkit.com"></script>
<article>
<div id="KiraRunkit"></div>
</article>
body
height 100%
overflow hidden
background-color sienna
article
margin-left 2rem
margin-right 2rem
// [INFO] Responsive iframe:
// https://medium.com/@mahbub_hemel/how-to-make-your-video-iframe-responsive-a8c5fda821ba
#KiraRunkit
width 100%
position relative
iframe
width 100%
height 100%
position absolute
/* [INFO] Instead of frameborder — http://stackoverflow.com/a/10831379/5951529 */
border 0
##########
# RunKit #
##########
# Run npm code online in browser:
# https://runkit.com
# Needs use theme-maker, that change styles:
# https://runkit.com/docs/theme-maker
notebook = RunKit.createNotebook(
# [NOTE] Id required, class will not work
element: document.getElementById('KiraRunkit')
# [NOTE] You need paste here content of your RunKit notebook even if it big:
source: 'var stringSimilarity = require(\'string-similarity\')\n\n\
var similarity = stringSimilarity.compareTwoStrings(\'Кира\', \'Кирк\');'
# [INFO] https://runkit.com/docs/theme-maker/untilted-2jxk2crve1p7 theme
syntaxTheme: 'untilted-028u85ijnoyr')
6. Problems
You can have these problems, when you edit your theme via theme-maker:
- If you need set exact color, You have to work hard, that make it in theme-maker.
- After the second and subsequent theme editions, changes may not display.
- Read notes in CoffeeScript file from previous section, that read about another limits.
7. Extra links