Neither available() nor mark()/reset() is called now. The new impl simply reads bytes one by one, and determines if the input is DER or PEM, and skips the non-data part of PEM at either the beginning or the end.
Since slow streams are now supported, buffering codes in keytool for importing and printing are removed. This can be confirmed by existing keytool tests, say, test/sun/security/tools/keytool/selfissued.sh, which contains calls like:
$KT -alias me -certreq | $KT -alias ca -gencert | $KT -alias me -importcert