There really is no conflict between these two sub-genres. There is a difference, even if we're splitting hairs. Charles De Lint first described urban fantasy with his story Dreams Underfoot in the early 90s, making it a relatively new genre, in retrospect to the times. In short, urban fantasy brings the fantastical into the mundane world or into the contemporary setting. It's another dimension, another time and place, a different universe with it's own rules. The magical invades our world, not the other way around. That's the more precise definition. Examples might be well associated with the book,The Mortal Instruments. Writers like Laurell K. Hamilton, Jim Butcher, Neil Gaimen, Deborah Harkness and Anita Blake's Vampire Hunter are prime examples of this sub-genre of fantasy. I think the important thing to remember is that in an urban fantasy setting, their world invades ours. Something crosses over and materializes. Sometimes this transformation happens with our knowledge, but many times it materializes unbeknownst to us.
They say (who's they anyway?) that urban fantasy is a Mixxmaster, mashup of science fiction, horror, dark fantasy, paranormal and magic realism where they all come together in a melting pot. Fair enough. What a mongrel, wot?
Portal fantasy. It's also been termed "low" fantasy. But who in the heck uses those terms to describe their work to publishers, editors or the reading public? You don't see it do you? My agent had no idea what I was talking about when referencing my works as such. She agreed that it might be a unique way to describe a fantasy sub-genre to a potential purchaser. My publisher blinked upon hearing the term, but did admit that she'd heard before. She confessed that it was doubtful that using the term might sway any reader decisions, or for that matter, having Amazon recognize it as a mainstay genre. Amazon is lazy--they fall back on urban.
So what's a portal fantasy? It is our intrusion into another world, be it deliberately or accidentally. We'll split hairs latter, but for now, think about Neil's Stardust. Where is the gateway or the portal? Why, it's across the stone fence, isn't it? Things become fantastic, abnormal, magical on the other side. Our world has not changed, it is still a contemporary setting. The magical land did not come from Them over to our side--we explored or blundered into it--we trespassed, so to speak
Some classic examples of true portal fantasies: Harry Potter: now what is platform 9 3/4 if it is not a portal, opening or gateway into another land and realm? There are even portals within portals in Harry Potter. Some will disagree with me on that. Alice in Wonderland: don't we have a mirror or rabbit hole? There's your gateway. The Bridge to Terabithia: step across that bridge and you're in a world of make believe. Hook: Isn't it the second start on the right that opens up into a sf-ish type planet/land? The Lion, the Witch and the Wardrobe: step through a closet and we're in Narnia. I can actually remember a Twilight Zone episode where a character marks off a section of wall to define a mysterious entrance into another world (De Lint, you might have been a little late in discovering it).Coraline: doesn't Coraline step through a secret door to enter another dimensional frontier?
How can Harry Potter split hairs on these two? Well, Harry travels back and forth from his world to Hogwarts, doesn't he? He's not a muggle, nor was he ever a muggle. He's a wizard in training. So when he comes back into his contemporary setting, he brings with him some special talents that are defined as magic. Therefore, to some degree, he impacts his real world, changing it every so slightly as his years in school progress. The Matrix could be consider a double whammy--we go in and pull things back with us. Stephen King's The Mist, is an example of our military opening up a forbidden gate (portal), and then suffering the consequences when the beast of that other world come barging in on our modern day setting.
Weird Science: We opened a dimension, and she steps through. Opposite affect here--we opened up the portal, but something came through it.
Tron: We trespassed. Portal.
Screamcatcher: The kids sleep under a decrepit, malicious dream catcher, and it implodes, pulling them into IT's world. It appears at first that their real world has turned into something strange and dangerous. However, it's not really their world--it's a separate entity upon itself. The rules of the world are governed by the Web and what it contains within it.
Kind of fun exploring these things. No harm done. No segregation. But I'm going to describe my trilogy as portal fantasies. Just you wait for the last book in the series called The Shimmering Eye. It was based on the true life scientific investigations of the Skinwalker Ranch, as reported by George Knapp, investigative reporter out of Las Vegas. I'll need a new genre for it!