I don't have a clear understanding of exactly what's going on, but I'll share what I know.
In the-bootstrap, partials/content.php calls the_excerpt() to get the excerpt for an entry (but only for searches). The codex says the_excerpt will include [...] but doesn't include a read more link.
I wrote a customized partials/content.php that always called the_excerpt(). Everything I tried to remove the link was unsuccessful until I wrote my own excerpt function (see last post in thread linked earlier) and called it instead of the_excerpt(). Other people on that thread were able to get the remove filter calls to work. Your mileage may vary.
While I was experimenting with excerpts, I found that calling the_excerpt() and adding a read more link would result in a double read more link, so it seems something is going in the-bootstrap to add the read more link, but I haven't been able to track it down. I needed to customize a copy of partials/content.php (with a different name) anyway because that's the only way I could find to force excerpts in a list on my home page, which I want to keep reasonably short (by default, the-bootstrap only shows excerpts for searches).
Maybe there's a better way to do it, but that's what I found that works. Maybe post on that thread and someone there will have more help.