I absolutely would reccommend SBT for beginner scala users. It's a must to use and understand it, as much a part of understanding scala as understanding for comprehensions, case classes, and if/else expressions.
Could be because Gradle up to version 2.x provided only Groovy for writing plugins and build scripts. Gradle 3.0 was released a few months ago, and provides both Kotlin and Groovy for plugins and builds, and even prefers Kotlin for writing plugins. Perhaps the "not-so-perfect" situation will change as plugin providers switch over.
I recently looked into Groovy's apparent popularity at #17 on the TIOBE ranking and found Baidu was giving a result 12 times too high and Yahoo a result 20 times too high, both of which would skew the ranking. Groovy's real ranking is somewhere below that of #50 ranked Clojure. These results are being used to promote Groovy as successful to the Apache Software Foundation directorship. I can understand Gradleware wanting to switch to a language with a seemingly more honest approach to promotion.
Joking aside, in Clojure this a feature, one of Clojure's theme is "embrace the host"(leverage java apis).
I don't know Scala but in Clojure you definitely need to become familiar(if you aren't) with Java if you are serious about writing productions apps in it.
Also, abstractions leak.
You needed to dive into Java to figure out something as basic as parseInt?
(.parseInt Integer x)
That may be what he means by dive into Java.
On the JVM, even if you stick to pure Java, you still need to figure out where and how the dependency resolver is launched before you can override its settings, which can depend on things like your build tool and IDE. But at least, adding your own certificates to the keystore/truststore is fairly straight-forward.
I don't have concrete examples to hand for the other rough spots but I recall hitting other areas of knowledge that are explained via Java instead of standing on their own. "The Scala Bar is like Java's Foo, but with these improvements..." I never learned the Java Foo and I don't really want to have to acquire a working Java developer's knowledge to use Scala. I'm using Scala and not Java. If you're writing docs for Scala and the reader needs to know something important about either Java-the-ecosystem or Java-the-language, please inline that knowledge.