A few comments:
1. Trade goods are going to be some of the most valuable "currency" for interstellar trade - no matter what currency or payment system a planet is using, trade goods they want are going to be valuable. So Free Trader's jumping from planet to planet will tend to do most of their transactions as barter (or equivilent of), with only the differences in value - IE, profits - being 'converted' to Imperial Credits.
2. In any type of transaction system, financial institutions understand the risks involved and allow for it. That doesn't always mean the merchants and other people they serve do. Secondly, the financial institutions often put as much of the risk as they can on their merchants/customers. That leads to two inter-related issues - A) merchants spending inordinate amounts of time and money to track down unpaid debts/bad cards/etc - I've had to send out $300 bills to customers for my time recovering a $30 'loss.' B) An aversion to accepting credit cards because they've been burned before. AMEX is well known in my industry for charging merchants all sorts of 'extra' fees for transactions that are "out of the norm." As a result, very few of my customers actually accept AMEX cards because the hassles aren't worth the return.
3. IIRC, there was an article in one of the early JTAS about the currency that Imperium "minted". It was done with some sort of special plastic and/or metal wires bonded together into a brick like form, then sliced really thin to make "paper" money.
4. Standards are all well and good, and even where there are competing standards, things are fine - as long as you have access to everything you need. As someone who lives in the US and subcontracts for a Canadian company, deals with my industry's various standards on a regular basis, and has lived in a foreign country for 3+ years, I can tell that things mostly work - until they don't.
While it is easy to find power converters, tri-band phones, etc for roaming across the world, not having these, or having something fail on you when you need it, and you're $#!+ out of luck until you can get what you need to make things working again. Ever been on a trip when your cel-phone battery died, and you didn't have your charger? Same concept.
That's the way I deal with IMTU - it all works, un-noticed beyond flippant GM comments like "you easily find the convertor you need", until I use it to make things interesting.
5. Even though the 3rd Imperium has been around 1100 years, you're also talking 11,000 worlds. To give you a reference to compare that to, there are between 3000 and 3500 counties (or county-like regions such as parishes) in the United States. When the Feds push some new regulation states and counties have to deal with, it can take years for things to be implemented - and that's with nearly instant communications. Blow that up to the scale of worlds, throw in the communication lags of jump drive, and even 1100 years isn't much time to implement all the needed standards everywhere - even less so if they're moving targets (and standards usually are).
6. Displays/Controls. Today's technology is really making configurable controls come to the forefront, even if they aren't ST:TNG style touchscreens. Take a look at the Logitech Harmony series of remotes for a good peek at what's possible. Even video game systems often allow people to program buttons and keys to their preferences. So IMTU even starships that have older technology buttons, dials and switches have personalization of those controls available.