It really is not that complicated:
There is clear and unrefuted evidence of prior vaginal injury. Since having a paintbrush shoved up her is also undisputed evidence of sexual assault--not "sexual" as in "for sexual pleasure", obviously, but sexual ASSAULT because of the area being assaulted, it's hardly a big leap to the conclusion that one was staged to cover up the other, as the use of a "paintbrush" is hardly explained in any other reasonable way.
But go ahead and ignore this, deny it, "Don't go there, pal," because we all know that this leads to the very small inner circle of the Ramseys. Can't allow THAT to muddy up the IDI theories.
And ignore the FACT that the linguistics in the ransom note clearly lead to the Ramseys. Patsy and John repeatedly used phrases from the ransom note when speaking extemporaneously in their interviews scores of times we can count. Patsy's exemplars are RIDICULOUSLY easy to match to the ransom note: "The two gentlemen" at the table? (COME ON! If you think she wrote that to MOCK LE, then ask yourself why the mother of a murdered child would do THAT?) Personal information in the note and crime were so obvious, even John remarked to Det. Arndt it was "an inside job". Even if John had no idea what had happened, he saw a copy of the ransom note brought to the home that morning by LE and HE SAID IT WAS AN INSIDE JOB. Why ignore this?
And why would anyone ignore that PATSY COULD NOT BE ELIMINATED as the writer of the ransom note by every handwriting analysis expert but one, including THEIR OWN PAID ANALYSTS? John said it. Pam Paugh saw the similarities and said it. Instead, IDIs keep harping on that Patsy wasn't ARRESTED, so that's proof she didn't write it. You've got it upside down: Patsy wasn't ELIMINATED as the writer, she was in the home, it was her child, all evidence of the crime leads to PATSY: her pen and pad, her paintbrush, her fibers, her handwriting and linguistics, her lies and obstruction of the investigation, etc., etc., etc.
What a coincidence! How lucky is this foreign faction?! Hanging out in the house, lolling around in the kitchen watching for the Ramseys while the rest of the gang is busy killing a child in the basement for...some reason...which ensures they won't get their ransom, after all....
There is NO EVIDENCE to put any intruder IN THE KITCHEN that I've seen. So that's pure speculation. In fact, other than a few cells of DNA--and those in the undies were degraded so that they have not gotten a full profile from them to this day--there is no evidence at all that doesn't lead to the Ramseys in the home the night of the murder.
There is not one piece of evidence leading to ANY intruder in 12 years.
NOT ONE.
But IDI's want to throw all that out the door because Lacy found a few cells of DNA at the crime scene, OUT OF AN ENTIRE HOUSEHOLD FULL OF PLENTY OF ARTIFACT, as any household has. What we don't know is if they ever tested THE CORD OF THE GARROTE, or the paintbrush pieces, or the alleged package of Bloomies withheld from the investigators for FIVE YEARS, among other things, for "touch" DNA. Did they do this? Did they find any OTHER DNA they can't identify?
We'll never know, because Boulder is way too deep into burying this case to ever tell us THE WHOLE TRUTH.
When they open the files and we can see EXACTLY what was tested, investigated, and what the results were, then maybe we can know the full truth of this murder investigation.
Until then, we're all just speculating because this case is FUBAR.