"long e" and "short e" in penalize
The variability between "short e" (IPA: /ɛ/) and "long e" (IPA: /i/ or /iː/) in words like penalize can be attributed to a conflict between the use of "long e" in the related word penal, and a certain tendency to use "short e" in a stressed syllable that is followed by more than one other syllable in the same word. (There is likewise a tendency to pronounce the letter "a" as "short a", "o" as "short o", and "i" as "short i" in the same conditions.)
The tendency to pronounce the letter "e" as "short e" in contexts like this is not particularly strong, and has many exceptions. Some of these exceptions can be categorized into classes (e.g. certain affixes, like -ly or -ness, add a syllable but never cause vowel shortening, so we have a "long e" sound in words like legally and evenness) but other exceptions appear fairly arbitrary (we have a "long e" sound in obesity, as in the related adjective obese, but a "short e" in serenity, unlike in the related adjective serene).
Most verbs ending in the suffix -ize use the same vowel length as the related unsuffixed word (examples: legalize and demonize, with "long e" as in legal and demon) but for whatever reason, penalize doesn't necessarily have the long vowel of penal. Possibly there has been some influence from the pronunciation of the word penalty, which as far as I know is pronounced with "short e" by all or almost all speakers.
I don't actually know how frequent each pronunciation of penalize/penalise is in different regions, but there are certainly some US speakers who say "PEN-alize"1, and some non-US speakers who say "PEE-nalize" (the Oxford English Dictionary gives the pronunciation as "Brit. /ˈpiːnəlʌɪz/, /ˈpiːnl̩ʌɪz/, U.S. /ˈpɛnlˌaɪz/, /ˈpinlˌaɪz/").
variation between dialects in the use of "long" and "short" vowels in other words
A somewhat similar example may be the pronunciation of the word privacy, which has a "long i" sound for most American English speakers, but a "short i" sound for many British English speakers (I don't know which pronunciation of privacy is more common in Australian English).
I don't see any connection between the two pronunciations that you mentioned. There is a previous question about the pronunciation of semi-: pronunciation US-UK in words like “semi”. Multi- and anti- are two other "prefixes" that show similar variation between /aɪ/ and /ɪ/ or /i/, with the /aɪ/ variants apparently more common in American English.
- Some American speakers might say something like "PIN-alize" and also pronounce pen as "pin". A merger between the "short e" and "short i" sounds before a nasal consonant (/n/, /m/ or /ŋ/) is known to be a feature of accents in the Southern United States.