SMA X HAD LTSS INTERSECTING RWY SEPARATION FROM SMT X. SYS ERROR.

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I HAD SMA X DOING TOUCH AND GOES ON RWY 21 VFR AND HAD AN SMT Y AS AN IFR INBOUND TO LAND ON RWY 29. I CLRED THE SMT Y TO LAND AND INSTRUCTED HIM TO HOLD SHORT OF RWY 21 WITH RWY LENGTH FROM THE APCH END OF RWY 29 TO THE RWY 21 INTXN OF APPROX 5200 FT. I DID NOT REALIZE THE SMT Y WAS CATEGORIZED AS A LARGE TYPE III ACFT AND COULD NOT LEGALLY HOLD SHORT BUT HE ACKNOWLEDGED THE XMISSION AND LANDED HOLDING SHORT OF RWY 21 AS REQUESTED. THIS CAUSED A RWY INCURSION TO OCCUR WHICH I DID NOT DISCOVER UNTIL AFTER REVIEWING THE 7110.65 ACFT TYPES AND CATEGORIES. THIS TYPE OF OCCURRENCE WOULD NOT HAVE OCCURRED IF THE PLT HAD ADVISED ME OF HIS TYPE ACFT AND THAT INSUFFICIENT RWY LENGTH WAS AVAILABLE TO LEGALLY HOLD SHORT. I WOULD REQUEST THAT PLTS INSTEAD OF ACKNOWLEDGING AND OBEYING TO AN ILLEGAL INSTRUCTION ADVISE THE TWR THAT THEY ARE UNABLE SO ALTERNATE PROCS OR ACTIONS COULD BE TAKEN; I.E.; GAR. SUPPLEMENTAL INFO FROM ACN 189134: I OBSERVED AN SMT Y ON LNDG ROLL ON RWY 29 AND APPEARED TO BE HOLDING SHORT OF RWY 3. 5000 FT IS AVAILABLE FROM THE END OF RWY 29 TO THE EDGE OF RWY 3. SMA X WAS IN THE AIR ON DEP AFTER COMPLETING A TOUCH AND GO ON RWY 3. AFTER INFORMING THE LCL CTLR THAT AN SMT Y IS A CATEGORY 4 AND LAND TO HOLD SHORT RESTRICTION WAS NOT APPLICABLE; THE LCL CTLR REPLIED; 'OH; I ASKED HIM IF HE COULD HOLD SHORT; HE SAID HE COULD SO I ISSUED IT.' WHILE THIS IS A VIOLATION OF INTERSECTING RWY SEPARATION PARAGRAPHS; I FEEL THIS COULD BE AVOIDED IN THE FUTURE BY PLTS NOT VOLUNTEERING TO HOLD SHORT OR CHANGE THE RULES BY ALLOWING PLTS TO HOLD SHORT ONCE THE APPROPRIATE INFO IS EXCHANGED (AMOUNT OF RWY AVAILABLE; WIND INFO; TIMELINESS OF INFO EXCHANGE). I MENTION THE SECOND OPTION BECAUSE IT HAPPENS ALMOST EVERY TIME BLOOMINGTON USES RWY 29. AN ACFT THAT ISN'T AUTHORIZED TO BE CLRED TO LAND RWY 29 AND HOLD SHORT RWY 21 OR 3 WILL VOLUNTEER TO HOLD SHORT OF RWY 21 OR 3 TO HELP THE CTLR OUT.