Let's be honest here, due to a limited number of sounds, Japanese can't replicate many foreign language sounds. This is common with many languages, by the way. English speakers have a lot of trouble with Vietnamese words that start with Ng, Japanese りゃ、りゅ、りよ, and even the ふ in 富士山 (Mt. Fuji).
First of all, you have to accept that your name simply sounds different when transliterated into another language. For example, Yochanan (Hebrew) became Ioannes (Latin) or Hans (German) or John (English) or Yanni (Greek) or Iain (Gaelic) or Evan (Welsh) or Jean (French) or Ivan (Ukrainian) or ヨハネ (Japanese).
Sometimes original spelling is kept but pronunciation changes. Sometimes the pronunciation was similar, but the language changed.
As for Scottish surnames, I'm assuming yours is difficult to pronounce because it's long. However, there's one really long Scottish surname that is well-known all over Japan and yet mispronounced every single time. You probably already know what it is, but here it is:
How do the Japanese deal with that tricky Scottish surname (McDonald's btw)? They usually abbreviate it to either マクド (Kansai), or just マク (Kanto). It's not weird, it's commonly done with other foreign business names (like ケンタ or スタバ) and although strange sounding to our ears, very normal in Japan.
English speakers usually abbreviate things long words, using letters to represent words ( NBC, FDA, SCUBA, TV, IBM ). As you probably already know, Japanese speakers naturally abbreviate using initial sounds (レモコン、テレビ、アニメ). And it's not limited to loan words, either. Many Japanese companies are abbreviated the same way. Nissan (Nippon Sangyo), Toshiba (Tokyo Shibaura), Nikkei (Nihon Keisai Shinbun).
Additionally, entire regions of Japan are abbreviated in a related way, but by using the same character. The Keihanshin area consists of one character from each of Kyoto (京都), Osaka (大阪), and Kobe (神戸) although they use the Chinese readings. Japanese call the 1995 Kobe earthquake the Great Hanshin earthquake. The epicenter was around Kobe and suffered the worst, but the entire Hanshin area was affected.
Okay, so now that you have that background on to your questions:
Would it be considered inappropriate in Japan to suggest to a staff
member / relative stranger to use my first name if they struggle with
Not at all. It's quite common for Japanese to use first names followed by the 〜さん suffix for foreign names.
Are there likely to be any complications (legal or otherwise) if I use an
alternate spelling of my name to make it easier for Japanese speakers to read?
Not usually, no. Especially if you just use the Katakana version of your name when writing it down, instead of the romanized version.
Legally, there is a standard way to katakana-nize MOST names as well as a standard way to romanize Japanese names. For super official purposes you may be required to use the official transliteration of your name. If your name isn't obvious to pronounce, learn how to write it officially in Katakana and there shouldn't be a problem. However, unless you're signing a mortgage, it generally won't matter. Some forms and documents will require you to write your name in Katakana ( Japanese speakers also do this with Kanji names as they can use different readings ), but it won't matter that much in real life.
If you're filling out a form like for getting something shipped to you on Amazon, just use what you want and don't worry too much. If your name is Victor, feel free to use either ビックター (Bikkutaa) or ヴィックター (Vikkutaa). Well-known names have standard pronunciations which may differ from yours, though. British pronunciation differs from standard American pronunciation and Japanese use one or the other, depending.
Really, the ONLY time you'll run into complication is if you're doing something super official requiring a Hanko stamp or like I said, getting a mortgage out or maybe opening a bank account, but banks usually are pretty good and have documentation about how to deal with it. Everything will be based off of your passport name in any case, and I'm sure they have an SOP somewhere that takes care of almost ALL contingencies. That's very Japanese.
As to what that official transliteration, we can't help you as you didn't provide the surname in question.