For example, consider the following sentence:
大多數真核細胞有高爾基體。
For those who are unfamiliar with biology, he/she may not know if 高爾基體 should be understood as (高爾)(基體) or (高爾基)(體)。Two avoid confusion, it makes perfect sense to use 專名號 and write the sentence as
大多數真核細胞有高爾基體。(With 高爾基 underlined, I am not sure how to type the underline here.)
Will this not be a good practice?
Proper name marks have largely fallen into disuse. That is because typesetting is difficult (as evidenced by your question) and that the text marked is usually understood by context.
我們有時看見一些書籍、文章中，已不使用專名號。這是因為印刷時比較困難，在約定俗成的情況下，現在已多不使用，並非錯誤所致。(古今標點趣聞)
Your concern for clarity is valid. But using proper name marks may cause further confusion in the case of eponyms. A Golgi apparatus does not carry any material attribute of its discoverer. Logically, it is just an organelle that just so happens to be discovered by Golgi. We all have Golgi apparatuses – what does Golgi (the person) have to do materially with our Golgi apparatuses? That is also probably why certain eponyms are no longer capitalised in English: e.g., abelian, newtonian, quixotic etc. Therefore, if you indiscriminately underline 高爾基, it may appear to some people that you are implying the apparatus belongs to Golgi (linguistically, attributive instead of genitive), much like 高爾基的帽子 (Golgi's hat).
I believe using parentheses also achieves clarity and is much more convenient (and commonplace) than using proper name marks.
大多數真核細胞有高爾基體（Golgi apparatus）。
范德華力（van der Waals force）是一種電性引力，但它比化學鍵或共價鍵弱得多。
I however agree that proper name marks may be useful in the context of classical Chinese, especially when annotating names of people and states. We may not have enough historical knowledge to parse the sentence correctly. For example, you need to be very familiar with the given name of Confucius (丘) to parse the following without the help of proper name marks:
孔子曰：「大道之行也，與三代之英，丘未之逮也，而有志焉。」《禮記》
Because more structural particles appeared, 专名号 is almost useless in current Chinese, but it is really useful in old Chinese as known as 文言文 because it is of help to 断句.
In modern Chinese, there are much more structural particles (such as"的""地""得") than those in old Chinese. It made 专名号 almost useless. For example:
（谢道韫）即公（谢安）大兄无奕（谢奕）女，左将军王凝之妻也。
——《世说新语·言语》
(This sentence means Xie Daoyun is the daughter of Xie An's eldest brother Xie Yi and the wife of General Wang Ningzhi.)
If we do not put 专名号 under 王凝之, the readers may think this sentence means Xie Daoyun is Wang Ning's wife(王凝/之妻, wrong 断句), not Wang Ningzhi's wife(王凝之/妻), because "之" also means "的".
But if we translate it into current Chinese, it will become:
谢道韫是谢安的长兄谢奕的女儿，左将军王凝之的妻子。
Since there are more "的", its meaning is clearer. Everybody can understand it.
In your example, "高尔基" is a foreign word. 译名用字 are very special in Mandarin. These words like "尔""斯""基""特" are not common in today's Chinese and when they are together, they can only form proper nouns. There is not "基体" in everyday Chinese, and students studying biology will not misunderstand it because they can 断句 correctly.
