One surprising omission here was Paradox, which uses its own in-house engine for (AFAICT) all of its grand strategy games (though this seems to apply only to their own studio(s); Cities: Skylines, for example, is Unity-based, and I believe Surviving Mars derives from whatever engine Haemimont uses for its Tropico games).
TaleWorlds is another studio that wrote its own engine for Mount & Blade (reused later for M&B Warband and its expansions), and more recently developed a new engine from scratch for the recently-released (and 8 years awaited) Mount & Blade 2: Bannerlord. The older M&B games were definitely niche, but Bannerlord's definitely notable going by the numbers (it's currently in the Top 10 games by concurrent players per steamcharts.com, though that seems to be tapering off now that the novelty's wearing off a bit; it also broke Steam's payment processing within minutes after launch). Early Access, but still an interesting example.
Yep, entirely new engine. Warband used a custom bytecode-like programming language that required Python scripts to generate, whereas Bannerlord uses C# and XML. The engine rewrite is a big reason why it took so long to develop, but it was well worth it.
TaleWorlds is another studio that wrote its own engine for Mount & Blade (reused later for M&B Warband and its expansions), and more recently developed a new engine from scratch for the recently-released (and 8 years awaited) Mount & Blade 2: Bannerlord. The older M&B games were definitely niche, but Bannerlord's definitely notable going by the numbers (it's currently in the Top 10 games by concurrent players per steamcharts.com, though that seems to be tapering off now that the novelty's wearing off a bit; it also broke Steam's payment processing within minutes after launch). Early Access, but still an interesting example.