I wouldn't blow this out of proportion. There are, inevitably, differences, and neither ACF or Railo are without bugs. I'm the process of porting several apps from ACF9 to Railo, and one from ACF9 to ACF11 (for now). The incompatibilities between ACF9 and ACF11, and the frustrations I encountered on the way, bothered me more than those I'm finding between ACF9 and Railo 4.2. The reason is that it seems to me the ACF engineers have been careless in the way they unnecessarily introduced bugs that weren't there before. And haven't fixed bugs that have been in the codebase for ages.
On the other hand, it is my impression that the Railo team, with much more limited resources, is doing a better job at maintaining a reliable CFML engine, and from what I understand of Gert's preso on Railo 5, is headed even more in this direction. It may be different. I may need to use the search and replace function in my editor to change a few hundred files, once I get to the root of an incompatibility. That's fine. What matters more to me is reliability, rather than slavish compatibility to ACF, because that's what my clients care about.
What I realized along the way in the process is that all along, I've adapted my code to ACF's quirks, failings, and way of doing things (rather than to Railo's). That's just how programming is. The fact that I need to make a few adjustments to my codebase (and perhaps file a few bug reports) when changing engines is perfectly understandable.
Here's my shortlist so far:
In Railo, getPageContext().include() isn't working the same as it does in ACF. I decided to work around this by using getPageContext().forward() instead, for now, which works in both engines. getPageContext() is an undocumented feature. I'm not sure if it is fair that I even expect this to work.
In Railo, I have trouble maintaining the varchar type on a QofQ for a value that sometimes looks like a decimal: 43.2, and sometimes does not: 43.home. The where clause then incorrectly selects 43.2, 43.20 and 43.200 as equivalent. I worked around it by introducing another field in the query without a decimal point. I think this should be reported as a bug, but I have yet to research it carefully.
In Railo, a mix of date types and timestamp types are not sorted in date order as I would need them to display a schedule of events (that could be date-based alone, or datetime range based). I'm working around this by changing the date type to a timestamp with a time value of 00:00:00.
In Railo, when generating PDF's using cfdocument, you need to add a div surrounding all other tags that sets the size of the page to get it to render correctly.
... and a sample of the other way around ...
In ACF9, 10, and 11, the ORM setting dbcreate="update" is broken on a particular app I'm developing, and has been for some time. The underlying SQL fails to generate a constraint properly, and takes the whole application down with it. I don't have a viable workaround, except not to use it, which is a PITA. I can't detect any sensible pattern to this bug. For instance, adding the entity "Invoice" broke the app. If I changed the name to Innvoice, it worked. I couldn't swallow such an inane workaround, so the entity remains named "Invoice".
dbcreate="update" works without a hitch on Railo, on the exact same code and database. So perhaps the workaround is to use Railo instead.
On ACF11, I've had repeated difficulty using the admin panel. I get automatically logged out whenever I try to make a change, like adding a datasource, or adjusting any other setting, and redirected to a screen inviting me to log back in again. The logs show a message "Unauthorized access suspected". The workaround is to clear the browser cookies (which I only hit upon after an embarrassingly long amount of time and frustration), which again is a PITA. I suspect that the ACF team decided to block attempts to administer more than one instance of ACF as a "security feature", but I haven't gotten to the bottom of this yet. No such trouble logging in and using the Railo admin panel.
On ACF11 pre-update3, I could not log into any of my applications. It seemed the session scoped variables that my code set on login simply didn't work. I was not at all pleased that I couldn't even test my apps on ACF11 without disabling the login mechanisms. On Railo 4.2, I have no trouble logging into my apps.
A further frustration with ACF11 is that although I pay for support, it is very difficult to reach them, and what I get back if I do has been woefully amatuer. Adobe makes every effort to keep you as a paying customer, but it seems to end there. If I'm using Railo as part of my business, I'd rather be paying Railo a base yearly support fee, just for the updates they already provide.