Just want to thank everyone for their comments and replies to this post.
Some of this discussion is simply over my head as I am not as educated in audio as others. That being said, this is my resolution....
After reading a few posts, I went home yesterday and started the test tones again. This was with the audyssey settings in place. At -25dB master volume and my left speaker at +3.5dB (set by Audyssey previously) my SPL meter was reading in the low 50's. As instructed by those in this thread, I turned the master volume up to 0dB. At this volume, my SPL meter was at 80dB. So, it seems this receiver can and does get as loud as my previous Onkyo NR787. I just had to adjust the master volume in the "test tones" area prior to adjusting trim levels.
I think my confusion on this is because on the Onkyo, you cannot increase the master volume while you're listening to test tones in the setup area. I assume that it defaults to 0dB and this is why I thought is was louder and more powerful from the start. Also, prior to my Onkyo, I had a Pioneer Elite AVR that did the same thing, so when the Marantz seemed quieter than the prior to AVR's, I immediately was confused and discouraged. Basically, it all came down to manual master volume settings within the test tone/level setting from one AVR to the other.
Additionally, I am happier with the Marantz SR6013 over the Onkyo NR787 for a couple reasons. First, the sound separation on Atmos tracks are clearer and more distinct. Even on non-Atmos tracks I hear subtle sounds that I never remember hearing before. Second, the audio delay... there is none. I had terrible audio delay from one source to another with my Onkyo. I was constantly adjusting the delay and it was the worst and most notable on the Xbox One S 4k Player. Most forums will say this is an Xbox issue and it may be, but the Marantz has zero delay, so take that for what it is.
In the end, it seems I still need to go a bit higher on the volume scale with the Marantz, but I'm ok with that if it means cleaner and more separated audio. Thanks again everyone.