First of all, Data.Aux[T] forSome { type T <: Type} can be written as Data.Aux[_] and is just Data
implicitly[(Data.Aux[T] forSome { type T <: Type}) =:= Data] // compiles
implicitly[Data =:= (Data.Aux[T] forSome { type T <: Type})] // compiles
If you put println inside handleMainType2
import scala.reflect.runtime.universe.{Type, TypeTag, typeOf}
def getType[A: TypeTag](a: A): Type = typeOf[A]
def handleMainType2(main: Main): Unit = 
  println(getType(main.data) + "=" + showRaw(getType(main.data)))
then
handleMainType2(Main(Data1(1)))
handleMainType2(Main(Data2("a")))
will print one of the following
(depending on how you define the type of Main parameter: Data.Aux[T] forSome { type T <: Type}, Data.Aux[_] or Data)
App.Data{type T = T}=RefinedType(List(TypeRef(ThisType(App), App.Data, List())), Scope(TypeName("T")))
App.Data{type T = _$1}=RefinedType(List(TypeRef(ThisType(App), App.Data, List())), Scope(TypeName("T")))
App.Data=TypeRef(ThisType(App), App.Data, List())
both times. So inside method handleMainType2 main.data has type just Data and Data1/Data2 are indistinguishable by type. What is distinguishable is runtime class:
def handleMainType2(main: Main): Unit =
  println(main.data.getClass)
//class App$Data$Data1
//class App$Data$Data2
So you can define
def handleMainType2(main: Main): Unit =
  assert(main.data.getClass.isAssignableFrom(classOf[Data2]))
with runtime behavior.
If you want compile-time behavior then you can try to make handleMainType2 a macro and use runtime reflection in the macro
// in a different subproject
import scala.language.experimental.macros
import scala.reflect.macros.blackbox
def handleMainType2(main: Main): Unit = macro handleMainType2Impl
def handleMainType2Impl(c: blackbox.Context)(main: c.Tree): c.Tree = {
  import c.universe._
  val clazz = c.eval(c.Expr[Main](c.untypecheck(main))).data.getClass
  if (clazz.isAssignableFrom(classOf[Data2]))
    q"()"
  else c.abort(c.enclosingPosition, s"${clazz.getName} <:!< Data2")
}
handleMainType2(Main(Data1(1))) // doesn't compile
handleMainType2(Main(Data2("a"))) // compiles
You can even make the macro implicit if you prefer not to make handleMainType2 a macro itself.
trait IsData2[D <: Data with Singleton]
object IsData2 {
  implicit def mkIsData2[D <: Data with Singleton]: IsData2[D] = macro mkIsData2Impl[D]
  def mkIsData2Impl[D <: Data with Singleton : c.WeakTypeTag](c: whitebox.Context): c.Tree = {
    import c.universe._
    val clazz = c.eval(c.Expr[ValueOf[D]](c.untypecheck(
      c.inferImplicitValue(weakTypeOf[ValueOf[D]], silent = false)
    ))).value.getClass
    if(clazz.isAssignableFrom(classOf[Data2]))
      q"new IsData2[${weakTypeOf[D]}] {}"
    else c.abort(c.enclosingPosition, s"${weakTypeOf[D]} <:!< Data2")
  }
object App {
  val m1: Main = Main(Data1(1))
  val m2: Main = Main(Data2("a"))
}
def handleMainType2(main: Main)(implicit ev: IsData2[main.data.type]) = ()
handleMainType2(App.m1) // doesn't compile
handleMainType2(App.m2) // compiles
Notice that handleMainType2(Main(Data2("a"))) or even
val m2: Main = Main(Data2("a"))
handleMainType2(m2) 
will not work.